That was the start of the nightmare for me. I "uninstalled" their software from my laptop and my icons disappeared. Realize that the only 2 programs I even started from them were start8 and fences. I never even ran any other program, however when it "uninstalled" it took out every last Icon. So I fired up the registry editor and saw literally HUNDREDS of registry pointers to "uninstalled" stardock apps. Rather than try to remove them all by hand I purchased an application to remove them. $40 and from what I gather from the logs, even that couldn't safely remove all the crap. So I finally had to system restore my laptop just to get it to work after merely installing stardock software. Drafted a memo to all my field technicians, stardock is off the approved vendor list for start replacement and classic shell is it's replacement. We build probably 750 machines a quarter and service many times that. I would estimate that since the o/s2 days we have probably sold 20,000 licenses for your software. That will not be happening anymore.
If you seriously think that there are not cracked versions that circumvent your activation technology, then you are insane. Leaving me to believe that you only want to squeeze your current customers for additional licenses because it is easier than getting in the car, going back to work, and "deactivating" a license on your work machine so that you are not nagged by your home machine. This is the same thinking that has made certain software packages "better to pirate" than buy.
It sounds like Fences may have set the desktop icons to hidden as it does this on a shutdown and then shows the icons again once it has loaded. This avoids a nasty visual on bootup where you have icons but no visible fences. Why this would have happened I cannot say, but to fix it you could have right clicked on your desktop and picked show desktop icons. The other possibility is if you were using the pages feature of Fences that perhaps the icons were offscreen. In which case arrange icons on the desktop would have returned them. Support would have been happy to help I am sure.
Regarding left over registry keys, would they be the settings keys for the products? As those are user data the uninstallers will not remove them as we have found customers tend to get annoyed when they uninstall to install an update (as some people do) and it wipes out their configurations. I don't know why would call them pointers, or why a product would be unable to safely remove them as they are simply strings or numbers stored in a database stored under the Stardock registry keys. Their existence causes no harm other than making the registry a tiny bit bigger.
I am sorry you had problems though and I can assure you that there are changes coming to the activation to make it more flexible as it seems someone set it up in a manner which was far from ideal. I made my opinion clear on the matter internally along with others and changes are currently going through QA testing.