This is a bit embracing but I've managed to get my Arduino stuck thinking it is a HID device.
I created a small test program on the arduino and then used Atmel's Flip software to upload the HID.hex file from this project http://hunt.net.nz/users/darran/weblog/cca39/
Arduino successfully thinks it is a mouse now and follows the program that was uploaded prior to the hex file swap.
I just put that file (Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex) onto an SD card an verified it against my Uno USB chip, without errors. So the file is OK.
You should be able to follow the wiring on that page (and get the SD card, heh) and re-flash the USB chip.
Atmega hex file uploader.
Written by Nick Gammon.
Version 1.9
Reading SD card ...
HEX files in root directory:
FOO.HEX : 2915 bytes.
ARDUIN~1.HEX : 20907 bytes. Created: 2012-05-17 16:16:06. Modified: 2012-05-17 16:16:06
--------- Starting ---------
Attempting to enter programming mode ...
Entered programming mode OK.
Signature = 0x1E 0x94 0x89
Processor = ATmega16U2
Flash memory size = 16384 bytes.
LFuse = 0xEF
HFuse = 0xD9
EFuse = 0xF4
Lock byte = 0xCF
Clock calibration = 0x8B
Actions:
[E] erase flash
[F] modify fuses
[L] list directory
[R] read from flash (save to disk)
[V] verify flash (compare to disk)
[W] write to flash (read from disk)
Enter action:
V
Choose disk file [ ] ...
ARDUIN~1.HEX
Processing file: ARDUIN~1.HEX
Checking file ...
############
Lowest address = 0x0
Highest address = 0x3D33
Bytes to write = 7414
No bootloader.
Suggest making high fuse = 0xD9
Attempting to enter programming mode ...
Entered programming mode OK.
Processing file: ARDUIN~1.HEX
Verifying flash ...
##########################################################
No errors found.
Try rebooting the PC. I've heard some crazy tales about Windows and caching USB info.
Ah, Windows!
Hehe, good advice actually. "Have you tried turning it on and off again"
Tried the reboot but still no change. I also have a mac nearby and its still acting as a mouse there aswell...
Unfortunately I don't have an SD card module and they are not that freely available here But the deadline for this project is within a few days so I'll have to find some other method.. I do have another UNO at home. Might be worth trying if i can flash the bootloader that way.
But if possible I'd prefer to get it working just using the Flip software. Can't be that hard?