I was in the same situation recently on a mileage run.

The outbound was HNL-LAX-IAH-ATL and the inbound was ATL-EWR-HNL.

I was in the 24-hour window for the inbound while I was in IAH, and no matter what I did I could not check in, because I think the system thought I was trying to check in for the IAH-ATL segment instead of the ATL-EWR segment.

As soon as I landed in ATL, I tried to check in again, and was successful, I was even able to REVUP the EWR-HNL segment