It must have happened when I was trying to ICSP that motor controll circuit, if things were working how I expected it should have only been connected to 5V, but its easily possible I screwed up and connected it backwards or touched it to the +12v line for the motor.
So far all I've done with the troubleshooter is confirmed that it only sees about 1.8V, but I'll try to figure out more with it when I get back to it. Also I might just try testing the transistor with the diode setting on my multimeter. I should have a transistor that will do the job, I have several single and darlington pnp and npn transistors on hand. I guess another advantage of a programmer you build yourself is that you can always repair it.