I had this same issue in 3.x, fences, but was able to solve it with the shortcut trick, but in 4.0 I have two folder portals to Sharepoint directories. One remains always and one disappears after logging out. I've tried direct links to the folder, links to shortcuts located locally, shortcuts on different local drives... it doesn't matter -- the folder portal to this directory always goes away after logging out. It's shown in the snapshot but using the snapshot to restore it doesn't bring it back either.
Thoughts on how I can make it so both folder portals survive a reboot?
This can happen if the drive is only accessible when you are logged in - in other words, it does not actually exist until you do.
Perhaps the best way around it is to map the location and folder portal to that map:
Stardock Support Manager