2007 GMC Sierra Electrical problems

I went to start my 2007 GMC Sierra Crew Cab 6.6L Turbo Diesel on Sunday after it sat for about 10 days and when I tried it acted like it had a dead battery. It just made one click and then nothing. I disconnected the main battery and put it on a charger for about two hours and then reconnected. I then tried to start the truck and still nothing. the instrument panel lights worked but they flickered repeatedly. The headlights worked and the radio worked on AM & FM but when I selected XM the radio said "Theftlock"

At this point I tried disconnecting each of the two batteries negative terminal one at a time and tried to start on each battery separately with the same results. I had the truck towed to my mechanic who pulled both batteries and charged and load checked them and they checked good. Since my mechanic was at a loss he had the truck towed to an Auto Electrical repair shop. They told me one of the batteries seemed to be shorted internally and that when I tried to start the truck it somehow caused the Body Control Module and the computer (PCM) to be damaged. They couldn't figure out what had happened but it ended up costing $953 for 2 new batteries, a new Body Control Module (BCM) and a re-manufactured PCM. Their bill said "Car shorted out BCM and PCM don't know how - vehicle does not have any short"

Since no root cause could be found I am concerned it could happen again. The truck only has 80,000 miles and I had hoped to keep it forever however now I am not so sure. Does anyone have a clue as to what could have caused this? Has any one seen anything similar?