On the off chance someone has experienced this problem and can hint at a solution.
I have a 50D and have been using ML on it for a long time, I also have the latest nightly.
I am well aware of the CF-battery protocol ;-)
All of a sudden all, and I mean all my batteries, kept discharging really quickly in the camera. I have a couple of Canon batteries and four others. I have tried three different chargers and the internal battery seems OK, i.e. date is maintained without the main battery.
I just tried two new third party batteries, with good Amazon reviews and these two exhibit the same phenomenon, i.e. battery seems to charge OK, when first in the camera all is OK, then the charge crashes.
Has anyone any ideas? I'm at a loss.