What an odd one. The powertop output looks rather funny. I do not understand your point about updating to 1.3. When you perform a full re-flash you should be re-flashing to the 1.3 firmware version.
Just to rule out ANY possibility of a hardware issue can you: 1. Remove the memory card & SIM card. 2. Perform a COMPLETE reflash, emmc AND rootfs. 3. Install powertop only. 4. Do the 'procedure' (offline mode, switch off, pull battery, power on again, wait 5 minutes then post the powertop results)