Try playing stepmania on the keyboard, your hands/arms/shoulders(/eyes) will be stronger. [media=youtube]Jg921i6PSQQ[/media]
But really, no idea what’s causing it. Might be the angle of your hand on that raised surface, I think placing the stick in my lap while sitting on a regular chair is most comfortable for me and most people. I never had this ache that you just described even doing intensive training on this stepmania stuff; my hands/wrists were just sore for a single day sometimes and never again after that. And I’m not a buff dude or anything of course.
It could also be just one of those sores that’s there for a few weeks and not the playing that’s causing it, just aggrevating it. But if it keeps being sustained like that you should see a doctor about it.