Not sure if this has been posted elsewhere already but I made an interesting observation last night when compiling a 200x200km are at levels 9,11,12 and 13.
At some point in the middle of the night geoconvert finished the job after finishing the last level 13 tile, went into a loop and started all over again with level 9. Hours later it's now overwriting all previous level 13 tile files again step by step. Impossible for me to say what exactly happened right then but maybe someone else observes a similar issue at some point.