"If" it's a glitch it's hardly earth-shatteringly disasterous....and not something warranting a system restore, etc.
Just post your problem details at support@stardock.com for assistance....
If you adopted a more reasonable approach....and determined that the non-hiding of inactive icons was not a threat to the sanctity of your computing environment you would have waited....to determine whether there was a SIMPLE solution available before you dived in with a System-Restore.
It's much like the [old] situation with Litestep...where Windows would pop up a message saying 'you must re-install windows' so people did....and they did NOT need to. It was a simple thing to fix but they still jumped in and claimed the sky was falling...
Yes, quite well, thanks...
If it were me I would have probably looked at effort vs. return ... as one does with most problem-solving and just waited and/or sought assistance online.
There was/is no real 'need' to waste 3 hours attempting to solve something that, as I already said, is hardly drastic or disasterous.....and certainly not a system-restore, which might or might not cause other issues worse than the one you are dealing with.
Usually when something goes gaga on my machine I search via Google for similar issues...and solutions....and failing that, I ask.
With a Stardock Proggy....a great place to go to FIRST is here, #stardock [IRC] and/or email the Company for support.
IF all that fails....and one simply MUST hide them icons, THEN [maybe] resort to a Restore....
But not before....