This post is partly to collect a bunch of snippets from other posts into one place, and partly a cry for help.
I have an Axon2 and I have a Pololu AVR Programmer. This is much faster and simpler than trying to program the Axon2 using the built in boot loader via its USB. In theory. In practice it is also a major source of stress.
For reference I'm on windows7 64 bit and using AVR studio 4.
After backtracking several layers of problems deep into forum posts I eventually found that this sequence has a reasonable chance of success:
Manually install three drivers for the programmer (two USB and one programmer). This solves the problem where windows device manager doesn't show com ports atall.
Go into the com ports section and make sure both ports are com9 or lower. This solves an issue with, presumably, some lazy code somewhere in AVR studio.
Plug the programmer into the Axon2 and turn it on.
Plug the programmer into the USB port of the PC and cross your fingers.
Sometimes it will light up one LED solid, and flash a yellow one - that means it's going to work and it's your lucky day.
Othertimes it will light up the first LED flashing green - that means it isn't going to work. Sometimes rebooting fixes it. Once (but only once) plugging it into a different USB port fixed it. Failing both of those I recommend going for a walk by a lake, which won't fix it but does make me feel better. Sometimes it starts working again after a couple of days.
If it does work, I seem to have the most luck ignoring all the instructions and choosing STK500 and Auto in the options.
So, presumably they aren't really shipping a product that only works on alternate tuesdays and I'm doing something stupid, but can anyone tell me what that is please?