When I connect the CBT to the USB port on my computer, the connection disconnects and reconnects repeatedly. the Devices and printer menu shows the Arduino Leonardo bootloader (COM9) appearing and disappearing rapidly. is this unfixable? There doesnt seem to be any way I can communicate with the CBT now...

I believe that's a driver or COM port conflict. I 've seen it before with other USB devices. Try a different or port or reinstalling the drivers.

I'm not an Arduino expert but I noticed there are to things happening when you connect the CBT. First it connects the boot loader (You can see what's happening in the hardware device manager (XP)) which gets its own COM port. After that it load the CBT itself which gets an other COM port.

Because my CBT got stuck in the boot loader it installed the driver for that and afterwards it always got stuck there. Kind of like your describing the connecting and disconnecting. What I did was to uninstall the drivers for the boot loader. Take the CBT out first! Put in the CBT again and wait till the CBT has actually loaded. This can take a few second. Then install the driver again.

This worked for me. YMMV.

I had the same problem and I couldn't upload code anymore. I took out the board from the housing in order to get to the reset button and followed this procedure: https://www.youtube.com/watch?v=plCxXwiUK-w
I uploaded the Blink scetch which is easy to find. After the succesful upload of the Blink scetch I could upload the CBT firmware again.

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Looks like your connection to CANBus Triple was lost, please wait while we try to reconnect.