I can only replicate something similar when I set overscan compensation on my system.
Do you get all the lines displayed when you choose "Double Size" in "View", "Video Frame"? If it does, the mixer probably isn't at fault.
Next is the renderer. MPC-HC doesn't do or detect overscan/underscan geometry compensation. That could be a problem in your case.
1:1 pixel mapping from the player itself should always happen when you disable "Keep Aspect Ratio", "Correct Monitor/Desktop AR Diff" and choose "Normal Size" in "View", "Video Frame". You can check that with the regular print screen button on your keyboard and pasting that image into an image editor. (The internal screenshot function of MPC-HC still needs some work.)
An easy one to try is in the options screen, you can select a different scaling method under playback, output. The PS types are generally very reliable in not reverting to point sampling, but can't do anything about system-wide scaling of course.
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