Aspect Ratio & Resolution Changing when Transcoding

[Cahill84]

O.k well that's helpful to know that the analog is 4:3 no matter what. With that said then I'm experiencing something weird. No matter how I set my playback ratio as, I get this weird box. Essentially it's like having two sets of padding. It's slightly annoying because I can tell the difference in the shade of black. Overlay manager plays the best, but the problem is not noticable in VMR9. I can't use Alt + PrtScn to get a picture of the Overlay, but I'm attaching the "boxed" picture provided by VMR9. It would be nice to expand it to the point as to remove one of the sets of bars. Thoughts....

PS- Yes I found the command line code for removing some many pixels from top and bottom, I can use the postprocessing.bat to sort through which shows and thereby use the right cutting.