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I think it may be that I/O is buffered so as to not drag down performance of the system if it had to keep writing often to the disk. First, how often are things written to the file. Second, there may be a way to force the write to occur...I think this may be your issue, and I think I've faced it before. I'll try to get back to you about it, or hopefully someone else has the answer already.
I guess in these coding cases, posting some source code is always useful if possible.
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