Arduino dropping midi signals

[Also, putting the 220 Ohm resistor in place of the 3.3k as suggested got me NOTHING coming in, so I went back to the 3.3k.

Now that's interesting. Makes me think the 4N28 is not the right opto here, or you need to play with that resistor. 220 may indeed be too small for the 4N28 yet 3.3k too high. I think it's worth trying something in the middle.

--
The Rugged Motor Driver: two H-bridges, more power than an L298, fully protected