^^^^What he said. I have also heard that even just leaving the key in the ignition could cause problems. Additionally...I was also under the impression that there was some sort of capacitor energy stored...even with the terminals disconnected. Every time I put in a chip I disconnected the terminals...then turned on the lights and turned the key to accessory. After waiting 10 seconds I shut the lights off, key off and key out, then did my chip swaps. Maybe I'm just smoking crack...who knows.
This may also sound silly...but does your battery charger have "jumping" ability? The reason I ask is because I had two batteries that tested good...the green light shown brightly...but I had a biotch of a time starting the truck. If I jumped the truck...it started every time. Ended up having a dead cell in one of the batteries. As soon as I went to new batteries...life was good. I know you said you put the batteries in another vehicle and that vehicle started fine...but unless it was a diesel...or a vehicle that has the draw that our trucks do on startup...it really may not have proved anything.