Yes. Same with me. No real solution as it gets more pronounced as we get older and more arthritic. If most of your (lifetime) playing has been at the piano (level), the muscles just aren't trained to handle this unnatural position for prolonged periods of time. Multiple manual organist fare a little better. I have a keyboard (VP770) on top of my organ (KeyB Duo MkIII) which has a flat top so that the VP770 sits directly on top of the organ without interfering with the organ controls. Since I only use it sparingly (the VP770), it's not a problem. However, in my studio where I have (two sets of) multiple keyboards on one stand, it's a big problem. In fact, I don't think I could play a live gig with that configuration.

The only partial solutions I can think of is to compromise a little and make the bottom KB as low as you can comfortably play it and move the top keyboard closer to the bottom one but further back so as not to obstruct the controls on the bottom one. Also, consider some arm/shoulder exercises to strengthen the shoulder muscles. You may need to consult a trainer for this. An alternate solution is, of course, an 'L' configuration (doesn't work for me). Good luck.

chas