For what it's worth, I too have had this problem. I'm currently switching my front-end from mamewah to Mala. So far, I've experienced it with the Atari 2600 emu's and Daphne. The background image shifts down and to the right, but the game list, snaps, etc., stay in their original position.
I have found a solution that works with my system. Note: I'm using Mala RC9 and a ATI Radeon 9600 video card. There's a display option in the video card menu that reads "3D Refresh Rate Override". While I believe Mala should correct the issue, this has solved my problem for all emu's.
Hope this helps!