I got a bat file from support, but the /enable parameter seemed to do very little in my boot experience.
The time differenct between the autostart link and the batfile in startup folder, seem to be nearly identical on an SSD, too fast for the parameter to take effect.
I created a scheduled task for windows, delaying startup with 1 second works for me.
Perhaps Fences or something in Explorer.exe is waiting for a network connection or some other DLL to load???
As the task is not started untill all other log-on startups are complete, fences is able to load without any problem.
Hopefully we can get an actual patch for the issue, but for now, scheduled task is a free and easy workaround.
Per user, workaround:
Here is a brief explanation on how to add a scheduled task.
You might be able to do some more scripting to create one for all local users, but for me the single user is enough.
I first disabled the original startup task using ccleaner (you can also do it with a 1000 other programs like it, just google disable startup program)
On windows 8.1 x64 (mostly identical for older windows, but some options might be slightly different):
start menu search for: Schedule tasks
Open the Task Scheduler Library, create task.
Give it a name (let's go crazy and use 'Fences'), set it to run only when user is logged on. Untick 'highest privileges' and 'hidden', as those two are not needed.
Go to the Triggers tab, select new, begin the task: at log on
Tick delay task for 30 seconds, you can even type in the selection, experiment with any amount of seconds and share your lowest score with us 
Make sure 'enabled' remains ticked, all the others are not needed.
Press OK to save the trigger
Next up, go to the Actions tab, add the path to your fences install dir (for x64 bit OS the default is: "C:\Program Files (x86)\Stardock\Fences\Fences.exe", for 32 bit remove the ' (x86)').
As parameters add: /startup
I'm not sure if this is needed, but I wanted to emulate the auto-start function as closely as possible.
You can customize the Conditions tab as you see fit, I would recommend you untick all the options here. Otherwise the task will only run on AC power.
Settings tab:
Tick:
- allow task to be run on demand
- Run as soon as possible after a scheduled start is missed
- if the task does not end when requested, force it to stop
Untick:
- if the task fails, restart every:
- stop the task if it runs longer then:
- if the task is not scheduled to run again, delete it after:
I hope this helps the other users with this issue and the developers to solve the problem.