I can say that even after running that bat file and uninstalling, then reinstalling from the given link, I still get this issue.
ruifungyip
Installed the provided build, restarted, still happens. Also, in response to @basj's question, no it does not happen when set to "Always place above". Additional information that may or may not be relevant, The primary screen is a laptop display, nvidia optimus setup. The secondary screen is a displaylink USB display. Main screen resolution is 1920x1080, secondary screen resolution is 1366x768
Notice that in my screenshot, some of the explorer windows have issues on the ribbon bar, those are the explorer which has been dragged from one screen to the other. (The lower explorer windows.) It should be noted that the smaller screen has a scaling setting of 100% while the larger side has a scaling setting of 125%.
As can be seen in the image below where the windows that look fine, have been opened on that monitor. The windows that looked bugged has been opened on one screen and dragged to the other.