So even though all of the desktop enhancements that I bought directly from Stardock are the problem of Parallels? No additional VM software, just the desktop package a couple of years ago directly from Stardock?
Parallels also licensed them so in the VM it will be reinstalling the ones from them. In other words your VM is reinstalling them not us. Either that or your VM isn't actually saving any changes you are making and thus rolls back to when they were installed.
Neither Start8 or ModernMix from Stardock are capable of reinstalling themselves once uninstalled.
The only other option is the uninstallers are not working at all due to some conflict between the two in which case disable the services and then reboot and delete the directory.