I can add Messenger to the exclusion list, and it correctly doesn't do the WindowsFX effects on the window, but the problem stays. The problem stays even if I unload WindowBlinds completely. The only way to get rid of it appears to be to uninstall WindowFX.
This is a little tough to explain, so I'll include pictures. Windows Live Messenger 8.0 (Build 8.0.0812.00) has a feature that allows you to hide the menu bar. When I have that enabled, my Messenger windows, seemingly randomly, develop an extended top bar where the menu bar used to be. If I move my mouse anywhere on that area, the cursor becomes the vertical double-arrow for stretching the window size. It's as if WindowFX only partially recognizes that the window isn't as big as it thinks it