I've had this problem before as well, mine would randomly dissapear in batch rendered sequences. I can't remember if and how i fixed it as I think it was before I upgraded my computer. I think it may have been a memory issue, does the output log give any errors? or there is a render analyse tool I think that might show you where the problem is. Is your machine up to spec in terms of memory?
Alan
Technical Director - Framestore
Currently working on: Your Highness
IMDB