I've never had a custom fit. I don't have arthritis problems but I do have history of problems with my right knee. I've only ever had the basic fit service at my LBS.

I would start with making sure your saddle position is correct. When you had your initial fitting, they should have made sure the saddle height is correct and dropped a plumb line from your knee to check fore/aft position. But even if they did that, it's possible that your position on the trainer at the shop is different from your position while actually riding -- you may be shifting forward or back on the saddle. Another possibility is that your cleat position is off, if you are using clipless pedals. At my LBS, this type of adjustment would be free, especially if the bike was still pretty new.

As for saddles, your problem might be caused by too much padding in the nose and/or a too-thick chamois in your shorts. But before you try different saddles, read about how to determine your sit bone width and whether or not you would benefit from a cut-out.

Good luck!!