To close this subject I like to give you a short summery:
First of all I'd like to thank Yves and Francis for their great support to solve the problem: Thanks guys!
As in most cases, the real problem was sitting in front of the Primer2 - me. I have initialized the device with one clock speed and than switched it accidentally afterwards to another. Bad idea, very bad idea!
The next problem was related to the freeRTOS port for the Primer2 that I used. This version was still based on CircleOS 3.7.1. After updating to CircleOS 3.8 and the above mentioned fix the Primer 2 was able to boot again from the battery.
Stephen