There is a security nonce implemented there – theoretically, if you wait some time (it should be like 2-4 hours) between opening the options and saving them, then it is possible the options does not save.
Otherwise it might be a server related issue, especially if it is not possible to replicate it a 100% of the time. Check if you have any object, memcache or any other database related cache active.
Let me know if you find a specific option that malfunctions every time, or a specific setup, which is possible to replicate somehow.