bad news - good news:
I changed RAM to KVR16N11S8H/4 (full height), however this did not solve the problem.
Then, I stepwise upgraded from Ubuntu 12.04 LTS to 13.10 and voila! rebooting problem disappeared!
Workaround in the meantime (before upgrade): I applied the function 'rtcwake' which was surprisingly fine also with 12.04 LTS (with WoL on).