I wanted to share my experience with an 2004 Silverado 5.3 4x4 auto.
I was contacted to tune the truck. I plugged in and started to scan, it would communicate with the PCM and validate the license but it immediately timed out on the boot loader. I restarted the laptop, checked fuses, went through everything. By then the customers battery was getting weak, when the battery weakened it would start to read as usual but kick back and fourth from high to low speed. We charged the battery and the boot loader fail message came back. I found that the customer had an aftermarket radio installed, Pioneer brand. When the battery weakened the radio wasn't interfering with the PCM and read. But with it charged, it was. Pulling the radio fuse didn't fix it because the power was tied into the OBDII port. However, we unplugged the aftermarket radio and it worked just fine. Something in the aftermarket radio was messing with the interface. I've always heard of the aftermarket radio warnings on the GM bulletins but ignored them. I always turn the radio off on every vehicle I tune, but even with it off it was still corrupting my initial read.
I hope my findings are useful to someone in the future. This was a new one on me.
Thanks guys!