I've been using Shell Enhancer with Windows XP for quite awhile without having this problem, but then it started to show up first on just one app (Secunia PSI) and then also on Outlook Express, and now it seems to be spreading to other apps, in fact most if not all other apps. The close button (the X button in the upper-right corner of the application windows) is grayed out and does not work. Also, in some apps, the minimize button (-) and the maximize button don't work either. The minimize and maximize buttons aren't grayed out, and they are animated when you click on them, but they have no effect.
These problems with the window buttons are consistent and repeatable whenever Shell Enhancer is running, and the button problems always go away when I close Shell Enhancer. I made no changes to the Shell Enhancer settings when this started happening or since. It seems to have started happening all by itself and has been getting more widespread by itself also.
I use Shell Enhancer mostly to control window sizes and for the task switcher, and I don't want to have to stop using it, but this problem has become extremely annoying.