Users attempting to troubleshoot the problem claim that resetting the controller (through the built-in pinhole reset function) and plugging it directly into the console (via USB) do not correct the error, with one user going so far as doing a complete system restore to no avail. The issue, however, appears to be isolated, but is still a concern for a number of gamers.
Update: Overnight, the issue has spawned an interesting development. Users are pointing out that the problem may be isolated to "knock-off" PS3 controllers. Joystiq has contacted Sony for an update to see if XMB 3.00 targets these fakes or if the controller issue is simply a byproduct of the controllers not being able to catch up with the new firmware.