Using Sonar 8 PE with Motif ES Rack and other hardware synths.
When I loop a section of a song, the first note of the looped section only plays properly on the first time through the loop. All subsequent times through the loop, the first note is cut off abruptly. 

It doesn’t matter how many bars are looped, nor whether or not the loop starts at bar 0 of the song.  It also doesn’t matter if the first note of the looped section is on the first beat of the bar or not… For example, I could set up Sonar to loop back to bar 2 beat 1, and the first note might not happen until beat 3.  It still sounds like my synths are getting a note-off message milliseconds after the first note of the loop sounds.

I do NOT have this problem if I just use soft synths in Sonar.

I’m using the Yamaha USB MIDI adaptor.  Same problem happens under Windows XP and Windows 7 x64.

Thanks for any advice you can offer!

Open up your affected MIDI track in Event View.  Make sure all the control messages are visible.  Start the loop, and look for the exact entry point at the beginning of the loop.  I’m betting there’s a stray (or missing) CC message in there that’s knocking it off.

Needless to say, this shouldn’t be expected, but it does happen…