I am not a doctor and cannot diagnose you, however you sound like you are experiencing what I first experienced when diagnosed with Fibromyalgia and then RA. I ran into the same problem with my first Rheumie in that he diagnosed Fibro first and, like you, I asked "what about my swollen joints". He then did the appropriate blood work, which showed the high inflamation levels, but not the RA Factor. So, after trying methotrexate and plaquenil for about 6 months with no effect, and also seeing a pain mangement doctor at the same time, I went to another rheumie who diagnosed me with Fibro and Poly-arthritis. Which means he is pretty sure it is RA, but nothing in the way of blood tests confirms it other than the inflamation.
So, this started 4 1/2 years ago and for about 1 year I was on Humira, stopping about 4 moths ago, and the Humira did help. Steroids helped too, but also caused me to gain 40 lbs in about 4 1/2 months....not HAPPY!!! But, I stopped the steroids, and have been off the Humira for 5 months now and I know that it was helping as my symptoms (Fatigue, joint pain in every joint, including my back, and joint swelling) have gotten worse. The problem is I have moved from Florida to Utah and can't get into a Rheumie until January 30th. So, in the meantime, I continue my Fibro meds and my pain meds, and try to find a job I can do with my conditions....not easy.
But, keep trying to find your answer. I have a friend who went 6 years of doctor after doctor trying to find her condition, only to find she has Lupus. So, don't give up, no one knows your body as well as you, and don't let them shut you down. You really do have to be your own advocate and make sure your doctors truly understand what you are going through every day. Good luck and feel free to contact me if you wish to discuss further.