I have this issue as well:
iMac 11,3 (2010 27", i7 chip) with bluetooth Apple keyboard, trackpad, magic mouse: this problem NEVER happens, before or after Lion upgrade. Never.
iMac 9,1 (2009 24", Core 2 Duo chip) with SAME models bluetooth Apple keyboard, trackpad, magic mouse: this problem happens FREQUENTLY, starting AFTER I upgraded to Lion, and persists with Lion 10.7.2. It happens upon waking from a long, not short, sleep. In System Preferences I have computer sleep at 1 hr, display sleep at 30 min, no screensaver ever, Ethernet on (I have a wire to my Apple extreme), Airport off. I have a bunch of USB devices connected to two powered USB hubs, and two Firewire drives.
I am coming to this thread for the first time tonight and will try some of the solutions offered.
Question: if one sets Energy Saver so that the computer NEVER sleeps, does the problem go away?