Back when I made all the mistakes in the world while setting up my M2-ATX, I had the +12v and IGN wires reversed, so it was pulling +12v through a 20 awg wire, and not only did the computer not boot very well, but the wire got very warm! With help from 2k1Toaster and Darque, I figured out that the wires were backwards and after I switched them it worked just fine (+12v is like 12 awg from amp distribution block).
Wire resistance makes a difference. Try running a larger wire (e.g., 8 awg) directly from your battery (make sure it's fused), and just use your cig lighter for the IGN wire. Also make sure your grounds are the same awg and short length.