I had the exact same behaviour (note: could be a totally different problem) with my first MS (v2.2, 280zxt dist, 240sx tps.) After weeks of hairpulling, I finally swapped in a friend's MS with the exact same settings, and it ran fine. Turns out that I had fried something with an unregulated power supply earlier on. My MS box seemed fine, responded correctly, everything displayed on the laptop was normal, but it wasn't working correctly.
Again, your MS box might be 100% fine, but it's nice to have a spare to swap in to check.