This is a known issue dating back awhile. I think daveyliam#3 is related. Known causes are:
When many blocks are changed at once, or too many regions are created too quickly

Known symptoms:
Flashing map (one state has the original, the other has the new state), changes are saved on exit
New chunks are added to the map very slowly, and may or may not save
post processing is not added accurately (lines between chunks, errors in transparency, etc)

These all still occur with 57814da in 1.7.10. I'd offer advice, but after working on it for countless hours over the past several months, I've got no helpful advice other than a possible security error or a disk throttling issue (utorrent has an issue where if the disk gets throttled, it can no longer write to it).

i know of this problem, and just like you searched for it a long time, but cant find anything that is the cause of this.