Anyway, I contacted the supplier and received a prompt and helpful reply from their tech department. The bloke suggested I follow the procedure detailed here: Home
This process did indeed re-flash the bad Uno but I am still unable to contact it directly via USB, so I'm still no closer to a fix unfortunately. I thought I ought to mention this in case it helps someone else. At least it proves that the 328 chip isn't faulty - when I plugged it into the USB afterwards it successfuly ran it's blinking light default sketch.
I didn't really expect this to fix the problem since we seem to conclude that it's a physical problem with the board but it was an interesting excercise to follow and has increased my nerd cred a bit 
I might take it to work tomorrow and show some of our technical boffins, some of them have used arduinos for work before and may be able to debug it with some of their fancy equipment.
Thanks for all your help and advice guys - appreciate it.
Cheers.