Not sure about this . . .
What is the measured voltage of your NiCad? How old is it?
Just in case, I recommend all the basic debugging like restarting your PC, etc.
I was originally using 4 AA batteries to power the axon but when they finally dropped below 5.35 volts they could no longer see the axon through
just an FYI - It's never a good idea to program an Atmega with a very low voltage, as on very very rare occasions it'll randomly cause a fuse corruption. A fuse corruption that affects the clock fuse will brick your Axon, a huge pain to fix.