I just tried an AVI file (DivX codec) and it worked. Haven't been able to recreate your problem yet

. I'll poke around and see if I can still, but have you tried un/re-installing it? The version I am using is from the Mac App Store (you can also download it from the mplayerx.org website). I am also on 10.7.3 / 1.0.13.
Not that it should matter, but just for comparison, which Mac are you using? Integrated Graphics or Discrete? Single or Dual Monitor setup? And if not a laptop, which connector are you using to your monitor (HMDI, mDP to an adapter, etc...)? Sorry we've been no help so far.
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EDIT:
Make sure the video does not have letterboxing burned in to the video. I was able to recreate your problem with a video that had the top/bottom letterboxing as PART of the video. (Black on top and bottom as well as sides) Then fill screen fixed it.
I don't see an option for that at first glance.