How long are you planning on running the device for? You could always save to internal drive of the RIO and then FTP the complete file to the host, this may stop issues you having with windows being its normal unforgiving self.
I've been doing just that - I log to the RIO and FTP it after the run finishes (I only need 2-3 hour logs) - that seems to be the cause of the problem (windows FTP capabilities). I'll test with proftp and see how it copes.
I can confirm it's a combination of two things.
1) Windows FTP handling - seems to only copy>paste the first version of a file unless you copy another-named file in between. Repeated tests show this, and the use of another FTP client confirms that it's not working correctly with the windows native client - people should be made aware of this!
2) When re-running the lv.vi, the initially displayed data is the old data, despite the file having changed (for definite this time) - in order to get the correct new data you must expand the tree on the left, at which point the new data is refreshed into the view.