I'm sorry to hear of this problem, and I don't have a solution, yet. But I can tell you that I'm having the EXACT same issue, AND it didn't start until I upgraded to Studio One 4.
My keyboard is a Yamaha Stage Piano CP33, and what you've described is identical to what's happening to me. I can, however, add the notes manually with my mouse, and they work fine. But using my keyboard is a staccato disaster. At first, I thought the issue was a reverse polarization of my sustain pedal -- something that's not uncommon. But after further investigation, I've determined that the problem happens with my keyboard when using it in midi mode.
Please write back ASAP. I need to know if you've made any progress to fix this problem.