1. Docks, shelves, and modules forgetting their position when screen resolution changes happen.
There are mechanisms in place for this not to happen, and as you are about to understand this is not as simple as you might think it is at first glance. 
First, are or were you running v24.4?
Anyway, there are two or even three sort-of conflicting issues here:
1. When you change screen resolution, WorkShelf has to make sure everything is still on screen otherwise you would not be able to access or even see that particular screen object and drag it back.
So, if you change to a lower screen resolution and this would result in, say, the desktop weather module now being off-screen, WorkShelf automatically moves it back into the available screen area.
Likewise, docks must fit on the screen in their entirety - WorkShelf will automatically reduce icon size to enforce this if necessary.
2. Desktop modules have different shapes and sizes according to the current theme. As such, desktop modules neatly arranged by the user in such a way that they are nicely positioned and don't overlap each other when using theme x, would or could overlap (or simply look oddly positioned) when switching to theme y if the size/shape of the modules was different and the modules remained in the same position.
WorkShelf thus remembers the position of the open desktop modules on a PER THEME base. Switch to a different theme and it will either auto-arrange the modules so they fit on the screen without overlapping each other (if this is the first time you apply that theme) or they will retrieve their previous position for that particular theme.
This is further complicated by the fact that you might actually switch to a different screen resolution, in which case the module positions remembered for that particular theme no longer apply. Therefore, the position of modules is remembered not only in terms of the current theme but also of the current screen resolution.
3. This was complicated enough for single monitor systems, but with the generalization of multi-monitor systems it became even more complex eheh. Now you also have to take into account the existence (or not) of extra monitors, their individual screen resolutions, etc..
Furthermore, you might want two docks when running with two monitors, one in each monitor, but only one dock when using a single monitor (e.g. when attaching an external monitor to a laptop, etc...) or some variation of this.
So, in v18.2 I added automatic multi-monitor profiles, a functionality that is enabled by default but can be disabled in WorkShelf Preferences -> General tab -> Disable multi-monitor profiles (although I have no idea why anyone would want to disable that).
This allows not only different dock/shelf/drawer positions for different multi-monitor configurations AND screen resolutions as well as the ability to enable/disable certain docks/shelves/drawers according to the same criteria. As you switch to a different resolution or turn monitors on and off, the previous configuration is automatically saved and remembered.
Desktop modules were actually excluded from the multi-monitor profiles and used a different method which did not take into account multi-monitor systems, but in v24.4 those too were consolidated into the multi-monitor profiles mechanism, while retaining the ability to be positioned differently according to the current theme.
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Warned ya it might not be as simple as you initially thought. 
One major wrench in all of this: Winstep applications are high-DPI compatible but they are NOT per-monitor high DPI compatible. In practice this means all monitors MUST have the same screen DPI (e.g. all 100% or all 125%) otherwise Windows will *literally* lie to the Winstep application about screen resolutions etc. As you can imagine, that can wreak havoc in this beautiful picture.
Not sure what is happening there, but I would need more information from you to figure out what the problem might be in your case (e.g.; perhaps the fact that switching themes automatically affected the position of desktop modules - or even the way the multi-monitor profiles work - led you into thinking this was an issue?).
There is also something else that might have something to do with it: from what I have been told by more than one Winstep user, the new version of Start11 (v2?) seems to have a bug with reserved screen areas (i.e. areas on the screen edges that are not covered by maximized windows) where it reserves an excessive amount of space thus squashing everything in the middle of the screen - at least this happens when Nexus Ultimate/Winstep Xtreme is also running (and I suspect other applications that also reserve screen areas).
2. The weather module becoming 12 hours out of sync. Showing the moon during the day and the sun at night.
I would need you to tell me your location, the location the weather module points to, and a log of the weather info retrieved by the module which you can obtain by going to the Weather Settings dialog, clicking the Get Weather button, and then navigating to C:\Users\Public\Documents\WinStep where you should find a file named Weather.log. Send this info/file to the Winstep support address or open a new topic in the Winstep forums.
Whether a moon or a sun appear as the icon depend on the local time information retrieved from the weather feed, and this can be provided in local or UTC. Since I live in Portugal, for me they are one and the same and I would thus never see this happening here, but assuming one when it is the other can result in what you are describing - it happened before with the Weather.com feed and was fixed at the time, but I'm not 100% sure about the MSN feed (which is the only feed still active at this point) as the code used to decode the info is different.
3. Gridstacks opening behind open windows.
Provided you are opening the Grid Stack by clicking an icon on the parent dock (which brings the Winstep application to the foreground), that should not happen unless the window above the Grid Stack is set to "always on top". I'm not seeing Grid Stacks opening behind other windows here.
Any steps to reproduce?
The last issue I hesitate to bring up (fools rush in where angels fear to tread), but I know from comments in this and the Winstep forum, it is important. If I am out of line asking please say so. I'm sure that there is more to the situation than I understand.
You're not out of line for asking.
Years ago before there was a Wincustomize, the default site for skins, themes, etc for different applications was called Skinz.org. There was a Winstep/NextSTART section there with HUNDREDS of different themes.
Unfortunately Skinz.org belonged to a marketing company called eFront. Unfortunately because a major scandal erupted when ICQ logs between eFront's CEO and other employees were leaked. You can read more about this HERE. To cut a long story short Skinz.org did not survive the scandal, which also directly led to Stardock's decision to create WinCustomize in order to fill the huge gap left by Skinz.org demise.
Right before Skinz.org lights were turned off, Shoggot (back then the admin of the site) allowed me to download the hundreds of Winstep/NextSTART themes hosted there (which I still have), but, despite this and all his goodwill, there was nothing I could do with those themes as I did not have permission from the respective authors to post them somewhere else.
As you can imagine, it was a really painful experience for me to see so many beautiful Winstep themes becoming lost forever.
Fortunately back then there were some minor skin/customization sites that also hosted a Winstep section, so some of the themes survived. As of 2025 I believe only Wincustomize is left in practice.
So, to prevent something like this from happening again, not that long ago and once I was able to, I paid a web developer to create a Winstep Gallery (not open to the public) into which I have been asking some of the theme authors to upload their themes into (it currently has a couple of hundred themes, including all the themes from the late Stephen Welsh aka WebGizmos, who I always considered a friend). This gallery uses the same logins/accounts as the Winstep forums, so that theme authors may retain FULL access to their themes (including the ability to delete them if they so wish). It supports screenshots, user ratings, comments, etc..., i.e. the basics.
Because I also happen to like Picco's themes a lot, I asked him multiple times to please upload his themes into the Winstep gallery. He NEVER replied.
So, when he posted those skinning questions and requests in the Winstep forums, I asked him yet again, but this time in public to see if I would at least get an answer. Despite the fact that he would retain full control over his themes, he refused claiming that he makes the themes for himself, only values the user feedback he gets and doesn't care a bit if they get lost forever. His themes, his decision (as was mine not to answer his questions/requests because of this attitude, but I am not even upset, just sad).
I'm sorry he is "punishing" all of you now by refusing to upload his new themes to Wincustomize, but - again - that is up to him.
The thread is still there somewhere in the Winstep forums for anyone who wants to read it.