The world saves fine... if you force it to (/save-all).
This problem has carried across multiple hosts and multiple pieces of our hardware (albeit the first one did have a genuine issue).
The first time I saw the problem the world had inherited ever lasting rain and thunder, no matter what the level.dat edits did, it ignored my changes and continued on. It also insisted on logging players in with empty inventories and creative mode (yet the server was saving the player.dat files when they logged out) I thought at the time this was due to faulty hardware that popped up whilst we were investigating it, so I transferred him to a closer data centre and setup his server again from scratch, this time with MCPC+ which stopped the leaks occurring and stabilized the RAM.
The second time I reset it up, I ran on pure FTB (no MCPC etc) and fixed up the leaking, it again inherited ever lasting rain and thunder. Again, the level.dat's were ignored and after 5 mins, the rain started and continued for hours. Over time the chunks began resetting and wrongly locating.
The first two attempts were done on FTB Unleashed 1.1.4.
The third time, I switched to DW20 (default server software), fixed up the world leaks with PermGEN changes (128MB), regenerated the world from scratch, reduced the amount of chunks loaded (view distance) .
It ran fine for 2 days, I thought "yay, finally fixed!"... Then Solex came back.
Now chunks are wrongly locating and regenerating again, from I can presume (from the information I have been given), these are occurring whilst the players are actively entering and leaving the view distance of the effected chunks. Villages are also extremely common and spawning 'everywhere'.
With this new information I'm starting to eyeball Mystcraft which has the Eternal Rain, Eternal Thunder and Villagers symbols, for the possibility somehow that may be involved. OR the possibility that somehow their connection could be causing it, which would be a first in my books.
During the entire time, the only errors that ever showed up were 'world leaking detected'. The DW20 pack had no leaks.
It sounds like the saving routines (every 3mins/player logout) are screwing up, but it's beyond me why this is happening, on multiple mod packs, so fast, so frequently and across multiple server locations, only for this poor guy.
I don't struggle with many servers when it comes to fixing them, but this guy has landed a right ticket on my desk. >.o