Yes. I have had this happen and I lump it in with the myriad of infuriating glitches I am referring to when I talk about the "Selection Bugs". Once it starts happening it will only get worse as you move forward. You can try going back to an earlier version of the project (I now have to Save As after pretty much every few moves). The other thing I do if that is not possible is I start locking the Pos/Data of all clips in the project and then unlock as a work (huge PITA time waster but it forces the clips to stay where they are).
In your case, because it is affecting the actual clip you are trying to move perhaps what you could try is lock the Data part of the clip only then make your move. I think when this happens it is doing some kind of processing/setting change on the audio in the background. By locking the Data you may be able to prevent this change from occurring.
Gawd... I'm getting angry just thinking about it. Grrr...
Good luck.