It is a strange issue, that is for sure. The sample you provided looks exactly like an old CRT with a bent pin in the cable.
Is the colour cast always green?
When I said firmware, I should have said firmware/BIOS. I know some manufacturers provide BIOS updates for there NVidia cards, and there is a thriving video BIOS tweaking community and toolset. You haven't said which brand of video card you have, or the exact model (memory size varies within the GTX 750 Ti range, for example).
I am in Australia, so have lots of PAL format files, but I don't have any MKV files in PAL format, let alone ones with odd resolutions. So can't test you issue exactly.
Does it always happen to the same files? Even after reboots of the PC? Are there files that match the criteria for failure above, but still work okay?
If the answers to that are Yes, Yes, Yes, then I suspect it is a problem with the ripping and re-encoding you do. Since you are re-encoding anyway, could you redo one of the bad files and force it to re-encode at 720x***. Does that still fail? Can you re-encode one to 720p (Progressive) and see if it fails?
Also, if the answer to the first question was Yes, could you make a small file that has the problem, and upload it somewhere for some of us to test? That may at least confirm it is a problem with the file encoding or not. If not, you may need to start looking at your TV colour management, the graphics card a bit more, or something else specific to your setup.
It still could be madVR having a specific issue with the re-encoded files though. As mentioned above, if that is the problem, the Doom9 forums will provide better support, and maybe even a fix. The latest MC has
madVR v0.90.16 included, and that version had a bit of Gamma work in it, and now has monitor calibration, and Color & gamma settings. Have you checked those out? They may be new since you first looked at madVR. (Not sure.)
It could also be the LAV Direct Show filters, based on some reading I have done at the Doom9 forum.