CS6 and all versions of CC recognize and work with MXF files without problem. If your computer does not recognize them, the question arises, are you running Ubuntu instead of Windows?
If your export match sequence settings now is mxf. Check your preview codec in the Sequence Settings. That is what match sequences uses.
Why do you want to use Match Sequence settings, that is for a quick review of your movie with a preview codec of lesser quality.
Thanks so much you guys. So I don't know what was up with my computer or my software, but, it used to be that I had to check the match sequence settings to get my project to export with the same video dimensions. But, I have now fixed it! Thanks so much! Now I have better quality and I'm doing it right