Maggot, the "ThumbsCache" folder is put there by Windows, not DX. It shouldn't make a difference if you delete it or not. The folder I was talking about is in your root DX directory, not in the Themes folder.
/Program Files/Stardock/Object Desktop/DesktopX/AlonTheme
Thats the path on my PC, just replace "AlonTheme" with your username. That folder contains your current theme that you are using. You can still try deleting this folder, and it might fix the problems you having with the theme, as far as the systray problem...I don't know what could be causing that, sorry. Also, I'm still using DX 2.10.014, they don't even list the changes in the .016 build so I don't think that would matter anyway. If you still having problems you can always try the Stardock Newsgroups or IRC, might get some more suggestions there.