When you play with alternate GUIs....shells, that is....and you incoporate animations.....then open and/or move something such as TaskManager [which itself has 'animations'...CPU usage, etc]...you can get all sorts of animation freezes. The graphic card chatting to the OS and saying "WTF am I supposed to be rewriting?" ...can have a hard time working out what to refresh/rewrite as a priority.
I may have an AGP8x 256meg card only taxed to 1024x768...but I get it.
I think the reason is a fundamental XP OS one. If you push the limitations of an OS graphically then things that were NOT envisaged by the OS designer can occur.
It's a fact of life that "shit happens", and hardly one to lament as a 'bug' or 'issue'. Think more of it as an 'inability' and you won't be forever asking 'why', as if the knowledge would solve anything or fix the 'issue'.
Example.
I totally whacked my GUI one day by setting a Litestep module to control my res and refresh and inadvertently set it to 1600x1200 @100hz ....not a good idea on a 15 incher. No, I didn't think...'ooh, why doesn't a 15 inch monitor automatically drop out of a 'wrong' res...or why IS THERE a 'wrong' res?" ....no, I simply said 'oops' as I realized I was doing something BEYOND the specs of the equipment.
When a per-pixel skin is being drawn by WB within XP it is emulating the effect [but not the mechanics] of what Vista will do, and that is well beyond what MS had imagined XP was likely to be ever doing.
Think of WB5 per-pixel as the ability to jump off tall buildings [something you are not expected to be doing]...but a side-effect is the odd broken leg or two. If you want to be one who jumps off buildings then put an order in for crutches....but it's still better than just standing on the sidelines with the default XP Luna crowd....