Hi all,
Dean Camera here, author of LUFA (the USB stack code the Arduino Uno uses).
Firstly, sorry to everyone for the wait in getting this bug fixed; I was not made aware of it (not owning an Arduino board - I collaborated with my own hardware with the Arduino folks to get the Uno board working) until last week. From then I was able to quickly provide a fix, but it took a few days for remote testing and integration.
The new firmware should be much, much more reliable; the Arduino folks disabled a critical compile flag accidentally in their code fork that would cause "control requests" made by the host to be delayed while serial data was being processed. That led to the troubles you have found; constantly sending serial data would break the virtual serial port.
I hope everyone is able to update their board firmware soon; don't be shy; It is impossible to break your board permanently if upgrading through the DFU bootloader. The worst that can happen is you erase the USB chip's application area without loading in the new firmware, which is very easily fixed just like erasing the main Arduino processor through the bootloader.
My apologies again for the wait, and in future if you have found a bug please don't hesitate to contact me directly so I can produce a fix quickly.
- Dean
PS: I'll be making some alternative firmwares for USB-MIDI, USB-HID and other classes soon.