I managed to fix this by selecting the notes that occur simultaneously, clicking on Note>Pro Guitar>Edit pro guitar Note and ticking the "split" checkbox. This normally 'splits' notes out of a chord box, displaying them as individual notes (I don't know if it alters how the game picks up the notes at all).
I guess either there was some sort of chord box interaction causing problems, or using the "split" feature bypasses whatever was causing the problem entirely, either way, it looks good now.
Mysteryem's post in Note inconsistently disappearing in-game was marked as the answer