Certain emulators auto-adjust picture slightly to the left?

[plantkingdom]

Fullscreen auto-adjusts slightly to the left?

(Running Mala)

Certain emulators auto-adjust slightly to the left (about an inch).  They are not centered and the empty space on the right is just a black bar.  I have no idea what is causing this.  Has anyone experienced this?  My desktop resolution and Malafe are both running at 1280x1024 and every emu is configured to boot into fullscreen.

For instance, MAME games run fine, perfectly centered and taking up the whole screen.  Nestopia games, on the other hand, scoot over to the left where I can't see about an inch of the game and leave empty space on the right.  So weird.

[rpgposer]

Are you sure that NESTOPIA isn't changing the fullscreen resolution?  I usually see this type of behavior with a resolution change, because of the timings associated with the new resolution.
I remember having issues with this particular emulator with fullscreen and exiting, so I switched to Mednafen and haven't looked back.