Sorry about your experience
To set the record straight, Chautauqua has no gate agents of their own, except in IND. So, the person that you talked to in STL was an American Airlines affiliate.
On a side note, Chautauqua used to have our own people as gate agents there, but that just changed awhile back. I know it's hard to do, but try to talk to the captain.
I don't think that CHQ has jumpseat priveleges with Alaskan, but I'll get back to you on that. I know CHQ's jumpseat chairman and will post the results of the inquiry here.
Also, this might be a little insight into your STL experience. I was flying with CHQ's chief pilot once, and the American Airlines gate agent wouldn't let us board the airplane even though we were positive space. She complained that things didn't match up and what not. I asked her what we could do to solve the problem. She got real upset and said " You need to have your so called leadership or chief pilot call us and get this rectified. You won't make any flight out of here until that is done!" I calmly got Bart, our chief pilot, over there and he ever so bluntly set her straight. I've never seen an American gate agent change her tone so quickly! It was priceless!
Needless to say, stay away from nonrev on American. I have their flight benefits and they suck so bad I haven't used them in over 5 years!