I think Prism99 has identified about 90% (or more!) of what might be causing your discomfort.
I know that when I sit too long - it is quite the project to get moving again!
Have you "compared" the positions you used while cross-stitching and quilting to see how they are different?
I love to sew - but I get this serious discomfort between my shoulder blades - even when using different chairs, machines, and/or tables. I have not been able to identify the "why" it gets achy.