I flew ATL-MHH a few months ago, and couldn't check in online (nor could any of my family members). I called the PM line, the agent confirmed the ticket was synced up, etc.

Turns out all I needed was a passport swipe, and the TA had no idea why it wouldn't give me a BP that just said docs required. Took her no longer than normal to get me checked in. My guess it's something as simple as that, hopefully.