I have exact the same problem. It seems that this bug is pretty old.
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I would not class it as a 'bug' per se`. If I had to guess (and that is all it is as I cannot test), it's an order of operations issue - Fences is not able to see something (folder location) as it starts.
What would be a good test is to - after the PC is completely booted and folder locations set - that you restore a Fences snapshot to see if it restores the desktop as you expect.
https://forums.stardock.com/486084/fences-support-faq#snapshots
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Sean Drohan
Stardock Customer Service Manager