Could be a combination of things...the way you are sitting; way you are holding your work; any number of things. Sometimes if I'm playing on the computer for a long period as well as quilting for a long period I'll have some of those issues as well.
I use a metal ThimbleLady thimble which has you pushing with the pad of your finger vs the tip of your finger. I find that way much more comfortable. I've never been able to hand quilt with a leather thimble although I've used them successfully in the past with cross stitch and needlepoint.
I sit in a comfy chair, have the hoop in my lap. Sometimes feet under me, sometimes stretched out. I move around ALOT when I'm quilting. Don't know that is necessarily the reason for no pain but other than poked finger pain, I don't have any with quilting.