I'm having the same exact problem in every company file i use. I'm running three separate company files. Rebuilding the data does help however the problem keeps occurring not after every check but fairly regularly. This tells me that its a glitch in your program and not a data problem. Does anyone know if Intuit has a fix for this yet?
If the rebuild data doesn't fix it, it could be a particular transaction. The snapshot uses different code than the rest of QuickBooks. It should of course be correct but occasionally we uncover some new type of transaction that isn't handled the same way - if you have something like that I'm very interested in hearing about it so that we can correct the snapshot.
Generally now when we find one of these it is something really weird like a check written for negative amount. QuickBooks allows users to do a lot of things that on the surface don't make much sense. But people do them and it should handle it consistently.