I am having an issue with a USB device that uses the ASF CDC framework running on an XMEGA 128A3U.
When the AVR is soft reset, for example by updating the firmware or the MCU resetting itself, it is not always recognised by the computer afterwards. I don't get any error messages but I can't open the COM port and the USB device itself seems to be disconnected (the PC can't see it), even though it is physically connected. Physically unplugging and re-connecting fixes the problem.
I have had issues like this in the past with USB when devices don't do a proper disconnect. I tried forcing a disconnect via udd_detach/udd_attach for 250ms and made sure the pull-ups were disabled, but it doesn't seem to help.
I am using Windows 7 x64 and XP x86. Tried a couple of different PCs. It could just be Windows handling of CDC devices.