maybe you missed something
It's a long time I use Shapeshifter without problems.
Maybe your brother installed EVERYTHING from the Crystal Clear DMG (which I use as default!). So, search in your apps folder "Set alphavalue4CC". It's the app which makes the windows transparent. You can edit it by your preferences, or simply delete it, as I did. In my iMac it solved the problem.
Also a tip: Be sure to have version 2, or later, of crystal clear, or iTunes9 will ask you for an update, and won't open.
I also suggest you to use other beautiful black themes of shapeshifter, which you can download freely from the site: They will reduce a lot your eyes' fatigue.