IMHO UA staff at EWR has an attitude problem. Not that anybody in Terminals A or C have great attitudes. That being said they should have tried to help you.

I had a situation where I used UA miles on Swiss and TAP. Out of VCE, TAP showed my res as cancelled. There was NO UA rep and nobody would help me. I had to buy a new tkt from VCE-LIS and was going to deal with the problem from LIS-EWR once I got there.

My situation had a happy ending as another check in agent at TAP said my res was NOT cancelled and I did not have to buy another tkt. So, ended up getting the one I bought refunded.

Bottom line it is very tricky when more then one airline is involved and reservations don't get queued over between carriers. It happens for paid tickets and for free tickets. Annoying in all cases.