I'm not 100% sure, but you might try this:
1) Load the VM
2) Goto Control Panel and UNinstall Parallels Tools
3) Shutdown Windows (don't restart)
4) Start Windows
5) Install the new Tools
6) Let it restart Windows
7) Now, Shutdown Windows
8) Start Windows and see if the new settings "stick"
It may or may not work. But cleaning out the old and ensuring the settings are written to the registry, then doing a fresh install on the Tools, and saving those settings also should do the trick. Good Luck!