Something like this happened to me on Tuesday (was flying DCA-YYZ-YQT the next day). I tried to check in and it failed 3 times in a row saying "Check-in Failed", and to get my BP at the airport. Thought for sure I'd get SSSS or something... but no. Fourth attempt worked, no issues, pre-check, etc. on BP showed up. Totally random.

I was not using eUps, it was a standard booked-on-ac.com J ticket.