The implementation for FileIOThread in Bukkit/mc-dev is really broken. It is a number of issues.

• The thread can stop before you have had a chance to add any tasks.
• The thread stops when there is not more tasks but does restart if new ones are added. Tasks are added after the thread has finished and silently ignored.
• The method to wait for data to be written blocks the main thread and is the most common cause of the "the server can't keep up"

Fixing this code removed most of the "the server can't keep up" messages for me.