This is exactly what was happening with my computer. It would get so bad that it was even occurring after I closed all other programs and only had a single explorer window open.
Everything works just fine with the handle limit. But now some windows seem not update and I would need to Alt-Tab or mouse over parts of it to refresh. It might have something to do with the additional registry mods of the GDI process handle and user process handle limit that was suggested ini the above link.
Are you experiencing any delay in windows re-drawing? If not, then maybe I need to look into those other reg edits.