You didn't answer the question. Are the batteries genuine BlackBerry batteries, or not?

If not, then the best next step is try with a genuine BlackBerry battery.

If both are genuine BlackBerry batteries, and one 9700 is fine with both batteries and the other has the same problem with both batteries, then obviously something is not right with the device. You indicate that you reinstalled the device software. So, if you are observing the same behavior with both batteries after that, and if the batteries are genuine, and if the batteries work fine in the other device, then the problem is hardware.