Sometimes, when I switch to (or from?) a skin that has taskbar transparancy, I can see the previous skin's taskbar underneath.
Some skin's top border transparancy is unclickable, meaning that when I try to drag a window, the cursor clicks whatever is underneath the border, like a desktop icon or whatever.
Some skins make some program's text unreadable or even invisible and I have to highlight it to read it. When I minimize and maximize or switch back and forth, the highlighted text is invisivle again. This effects the text and sometimes the grid in some download managers, within some program's windows, not the pull-down menus. General programs like IE don't produce this but others do.
Not all skins produce the errors above. I would say on average half do but the other half work fine.
Other problems I'm having:
Sometimes I have to apply skins twice because instead of switching they sort of merge with the previous skin, especially around the edges making the minimize/maximize & close buttons difficult to see or use.
Also when changing skins I can sometimes see pink edges along the top.
With WB loaded, after opening the display properties in control panel to change a setting like the wallpaper the window goes all white and hangs then I get a rundll32.exe error and it won't close.
Changing skins always makes IE crash so I have to make sure I have no websites on my desktop before I change a skin.
Some programs, like emule have an extra button in the top-right corner which become detached when using any type of skin.
And lastly, some skins make my pc reboot.
That's it, I think.
My system info says my pc is capable of per-pixel stuff if that's of any help.