When I first got BS3 I had the same problem and thought it was due to running BS2 and BS3 at the same time. I was doing a of of transferring of recipes at the time. Now I use BS2 for storing a couple hundred recipes that I may, or may not, ever use and BS3 for my regular brewing software. I sometimes have both opened at the same time without a problem.
Oginme, who I consider to be "The BeerSmith Guru", posted in the past that when he has this problem it appears to be related to Windows updates shutting down the computer without properly closing the program. This makes sense to me because, when I had the problem occur, I had some serious performance issues which have since been resolved.