I have not personally seen this occur. However, a few ideas:

The August 2014 Cumulative Update (Hotfix) noted the following issue:

http://support.microsoft.com/kb/2883080

Assume that you use Save As to save a project file with a new name in Project 2013, and then you close the file. When you reopen the new file, the value of time-phased actual work has been changed unexpectedly.

You might try installing the CU to see if that fixes the issue.