I have had the same problem trying to access financial data back and forth between desktop and laptop. I ended up with a real mess last tax time. Finally, I had to go to an old backup and reenter everything. I hope I never need an audit trail. I think that the problem stems from the time delay syncing between computers. It seems not to happen when I leave time (several hours, although it could be less) between accessing data from the two computers.
As noted above, I had my financial (Quickbooks) files overwritten by older ones betweet WindowsXP and Windows7 overnight. A full day's work had to be reentered. Bittorrent has been removed from my system pending resolution of this problem.