I am also having issues with this. I qualify 100% and even called before I booked the flight to ensure I qualified. I have called SW x7 trying to resolve this issue. I have a flight this Friday in 3 days that I need a companion pass for and the agents over the phone can't help me. THIS IS AN ABSOLUTE DISASTER. They keep pushing me off to email (up to 10 days to respond) saying they will call me back (they never call me back) or to call back later. My friend got the same deal no issue, not sure why we are all experiencing issues. I didn't get a confirmation email that I qualified but when I called to follow-up, they sent me a confirmation email and stated that I indeed qualify, but phone agents can't change the settings UI to add in a companion pass. It's something inside the internal system that I need to be added to to enable assigning a companion pass.
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