What happens if you open ArcMap > File > Open > Browse to the corresponding MXD file and add it?
Also try to show the extension of the known file types and verify if ".mxd" appears twice.
If it appears twice, you should delete one of the ".mxd" from the filename.
Hi Micheal. I honestly forgot how I fixed that...I seem to recall disassociating .mxd's with arcmap, rebooting, re-associating them, then another reboot. I've been calling tech support for these types of issues lately, and they can usually figure them out.
I figured this out by unchecking "run as administrator" for ArcMap, not really sure how it was ever enabled as I honestly don't think that I did it at any point. This also resolved another issue where I could not see any mapped network drives in ArcCatalog i.e. E:, G:, etc. -- ? unchecking run as admin on the .exe for ArcMap solved both of these issues, this was after updating to 10.6. Hopefully this helps someone else.