FYI if you E-file your taxes, it eliminates most of that BS. I had some paperwork problem almost every time I filed my taxes the old fashioned way, but for the last couple years Ive been E-filing them, and I get a notice within the day, sometimes within the hour saying they have been accepted and such, or rejected if I screwed up. Way more pleasant than mailing everything off.
Your experience sounds almost exactly like several I have had with the IRS.
Whaddya expect though, its a huge huge bureaucracy full of troll like people.
Eventually, it will get done correctly, but only after they grind your bones to make bread.