Having exactly the same problem here in Amsterdam. After upgrading to 2.6.1, cron fails with:
PHP Fatal error: Maximum execution time of 120 seconds
While we did increase this time. Phpinfo() shows that the max_execution time is 5 minutes now, but somehow Moodle's cron job keeps failing with the 120 seconds error. Where is this limit set?
Changing to the experimental backup format is not the answer I was looking for.