Julie,

Pretty much every mouse manufacturer has different mouse drivers; they all access Windows architecture to varying degrees. No doubt 'Intellipointer' is the same. I also suffer from RSI, but I do not use acceleration anyway as it makes the problem worse for me.

I am quite happy with my Logitech Trackman Marble+. You might consider trying out some other mouse form factors -- trackballs, gyro mice, etc. -- to see if one of them helps your control.