When I started my 1st job at a Regional, I discovered on my 1st attempt to non-rev home during training that I was on the "no-fly" list. This was in November 2003.
I freaked out, but I was removed within two weeks after sending a copy of my passport and birth certificate to the DHS. And yes, I was told by my new company that I had 90 days to get my name removed from the list or I would be terminated.
I find it hard to believe they would be taking this long to remove someone unless there was a legitimate reason.