I had this problem in a simple 3 track test I was doing one time.
1 bass, 1 guitar, 1 instance of SD3.
The track played fine, but when I froze it, or exported the project, some of the hi-hat parts were missing. Just gone, even though they were present during playback.
The only way I could resolve it was by doing a real time export. I started this project in 8.5, and to this day, right on up to X2, if I open it and try to export it, the same midi notes are silent, yet I hear them during playback.
Unfortunately, sometimes things just get corrupted.
Good luck.