I have the same problem.
My chunk sizes vary between 1 and 5 megabytes.
I think it would be better to have one file, one chunk (or fewer files). I think that mineserver does'nt read them as fast as every user interface wants to have this chunks.
Sometimes, before a chunk is regenerating due "missing xPos or zPox", the blocks which I build disappear. Then, I can't chat, and the whole server is uncontrollable (I can't enter commands). After 1 or 2 minutes, it is all okay... And one chunk is replaced

Okay, I'll try to modificate the actual code to save it in other ways than the "normal" mineserver does.
Will report any success here.
thegk01