I built a new firmware, uploaded it and flashed it to the board. Unfortunately it doesn't work, but that shouldn't be an issue as I can upload another.

Except that I can't. The usual boot loader menu comes up, but it doesn't wait for me to choose option 1 or 2 to upload a new firmware, it just instantly says "you choosed [sic] 3"
and then goes on to boot the faulty firmware.

So my Carambola is effectively bricked. Any ideas why the boot loader has decided to go tilt like this, and more importantly how the hell I get it to accept my input so I can get control of the thing again?

that means that your module console RX signal is low level or not connected to serial port.
eq your serial port always get 0x00 symbol and goes to menu number 3 (default) without any pause

Thanks for the super fast reply. I think you're spot-on; looks like my serial dongle has a hardware fault. What a relief - thought I'd fried the Carambola and was going to have to start fooling around with a bus pirate in JTAG mode

Instead, it looks like I either quickly hack up some AVR firmware based on LUFA to make a quick-and-dirty serial port this evening, or go to the shop in the morning and buy a new dongle.

Ace call though thanks!

Hooked up a bus pirate in transparent mode and it didn't work. Tried a link to 3v3 to prove the point. THAT didn't work. So now I've got a fault Carambola yes? Well no actually.

I'm SO embarrassed to admit that once I put a little pressure on the Carambola SO IT WAS PROPERLY PLUGGED INTO THE DEV BOARD, all started to work

The idea was right - poor voltage on the RXD pin, but the reason was just my complete incompetence.

Lesson learned!