I have Vista HP/64bit SP2 on my back up machine which didn't have DX installed, so I did a bit of testing. (It's what I do.) I installed the free version of DX 3.50 downloaded from c|Net. The install went normally and everything worked, all included desktops and widgets ran , although I couldn't get silica weather to find my zip code. I then uninstalled it through Add/Remove Programs , my least preferred method, and reinstalled.
I loaded the 3 desktops and a widget or three, still no errors, and then uninstalled with Revo Uninstaller. After running the programs own installer, Revo found 169 reg entries and 160 files/folders(all in Username/AppData/Local/Stardock/DesktopX) This is why I use Revo, instead of Add/Remove.
It appears that the installer is working and the uninstaller, though leaving a lot of debris behind, will still let DX install again even with the left over reg keys and AppData. All tests included Client and Builder modes. At no point did I even reboot between installs. I therefore conclude that leftover keys and data shouldn't be a problem unless they are corrupt.
I know this may not be all that helpful to the OP, but it does more or less rule out a bug in the free DX 3.50 on Vista.