First of all, I would like to make it clear, the Arduino behaved like this out of the box.
I just now flashed my atmega16u2 with the hex code you mentioned.
First I had to install the driver for it (which is in a folder in the install path of the FLIP program)
Then I was able to use FLIP to write the program.
Unplugged it, plugged it back in. (The L LED still doesn't blink, it's still ON all the time).
Tried to install the Arduino drivers, and this time it worked.
Now the Arduino lists under COM ports as Arduino UNO(COM3) .
I started up the IDE, opened the Blink.ino file, selected COM3 as port and Arduino UNO as board.
Pressed upload, and now I get another error :
"avrdude: stk500_getsync(): not in sync: resp=0x00"
While uploading the RX led flashed, But the L led is still on, and the TX led doesn't do anything.
Found a thread on this subject :http://forums.adafruit.com/viewtopic.php?f=21&t=32708&start=30
But nothing suggested in the thread worked, I get the same 'advanced output' as in the thread.
So yeah, I think mine came with both chips unprogrammed. Manged to 'fix' the atmega16u2 but I have no device to burn the bootloader onto the main chip. I have ordered a second Arduino Uno from another site. I read i could use a working arduino to burn the bootloader on another one. If the guys at Iprototype can't help me out, I'm gonna try to fix it with another Arduino.
Thanks everybody for trying to help, now I'm gonna ask Iprototype what to do.