I had the issue on a 2008 Macbook Pro running Leopard (which is virtually identical to the 2009 ones). When it happened it also affected my NI Kore 1 audio-interface, so I assume that any USB audio-interface would be from that point on. Only restarting the Mac helped. All non-audio relation USB functions kept working (Midi, mouse, etc).
The reason why we suspected Parallels/VMware in the past is that the few people who reported it (including me) had that installed at some point (even if it may have been uninstalled it often leaves its kext system files on your system).
Additionally Apple published change-notes about the OS X 10.6.6 *Beta* stating fixes for exactly this configuration of USB with VMware/Parallels. If these changes made their way into the release is unknown though (nothing mentioned in the change-log of the release).
One problem with getting to the core of the problem is that different people seem to be talking about different issues. One user found that reflashing his firmware (with the same version he thought to already have flashed) helped: http://www.rme-audio.de/forum/viewtopic … 837#p53837
Since I still have the Leopard installation around I could try to run it on my current 2010 MBP to see if it's related to the installation or to the hardware. But knowing that the 2008/09 Unibody Macs were "lemons" (I had mine replaced 2 times, plus 2 replaced Logic Boards) I tend to suspect the Macs more than software setup.