the only things I touched where system icons, before CandyBar came out in terms of editing system files. Then with CandyBar changed them again, then restored originals. The other issue is that my finder isn't changing back, and my trash can keeps changing between original and last modified one. Other then that I guess I've played around with themes, but removed them all. I run ShadowKiller, and that's about it. I was thinking of doing a clean install since I did an upgrade from 10.1 to 10.2 but haven't had the time, and can't be bothered recusomizing preferences, etc. The problem happened as a result of the upgrade to x.2.3 but I'm not too bothered about it so if it's not fixed in any future updates then I'll just wait for 10.4 to go with a clean install. However fixing now would be most useful.
I've read that others had the buttons appear indented because of missing shadow so I'm thinking my missing buttons might just be a different version of that bug. 😛