Craft book has an auto chunk loader which is loading blocks but not enteties which means if you got a cobblefarm (im so sorry xD) the items directly get unloaded and dont vanish, if someone gets near the farm all the tons of items that have collected are getting load and the server is crashing.

Again, im so extreme sorry, that happened to my co-op server today so i know what the problem is

The only way to clear that problem is deleting all the items.
best would be for me to make a pressureplate triggered start or just removing it

That could defiantly be an issue Might have to change the perms for players as auto cobbling, using pumps, the teleport signs etc. don't seem necessary and are really not very vanillary.

Well, then I just must ask, if you broke it, fix it. Cause the server is laggin all over everyday...