I had a similar situation once in LAS trying to get on an UAX EMB120 to PSP. The gate agent basically didn't know what he was doing and wasn't interested in finding someone that did. There were no pilots anywhere around and the agent wouldn't let me go down to speak with them.

I missed the flight but had four hours until the next one. I ended up going down to the ticket counter (past security) and plead my case to a gal working the counter. She did some magic on her computer and gave me a boarding pass like it was no big deal.

Moral of the story: When you run in to an uncooperative or clueless gate agent, don't get mad and don't give up. The OP did the right thing by tracking down the Captain. If that doesn't work, see if you give find another agent to work with.