While remastering the Bej3 soundtrack I ran into a rather bizarre issue with one instrument's NNAs. Basically only every second note was playing (even though the NNA was set to "Continue"). I could only fix it by setting Duplicate Check to "Sample" (instead of Disabled) - which is not quite how it should work.
OpenMPT team, do you need a repro case? I should be able to create a small .it file for you to check by deleting everything else. (.......) In fact, here it is.
I coulda posted this to the bug tracker, but I didn't have an account nor could create one. O:)