I am experiencing the same thing - exactly as described above. I also notice that in addition to running very slow, delayed reaction to any command, it is failing to run Rules.
Tried trashing the mail icon from the dock and launching from the app, no change. Repaired permissions, restarted, no change.
The strange thing is that it started yesterday when nothing else on the computer was changed/installed/updated. Been running 10.6.1 since it came out. Mail was working very well until this "Drop Shadow/multiple Message Viewer windows" problem began.
What is it?