FOUND THE SOLUTION!
At least for me. I had the exact same issue come up today. Tried all of the suggestions on this thread, but nothing worked. Then, while looking through my mail folder (user/Library/Mail) I noticed several "Messages" folders, the main one and a couple other with long extensions tagged on the ends of them, "Messages-T0x1018b94a0-3bLNOj". I also noticed that two of the three Messages folders had nothing in them, while the third and last one did. On a hunch, I quit out of Mail, deleted the two folders with nothing in them and renamed the one that had files in it, ie. "Messages-T0x1018b94a0-3bLNOj" to "Messages". I had to do this in each "POP-" and "Mailboxs" folders I had an issue with. Once I opened up Mail again, viola! It's a Christmas miracle...all of my blank and then disappearing messages are back.
Hope this helps everyone else with the problem.