I have found a strange corner case which partCombine doesn't handle correctly. I ran into it setting a complex orchestral score, but I've narrowed down the demonstration to something more reasonably sized.
In this example, I have to do the known workaround in bar 2 of adding invisible grace notes when one staff has one right after a time signature change. The bottom line represents the piano part (with the visible slashedGrace), the top two represent two clarinets, and the third line is a partCombine of the first two.
Once this happens, partCombine starts putting slashes on any unison flagged notes from that point onward. Quarter notes are fine; 8th, 16th and so on get slashes.
The critical thing that triggers this is that one of the two combined parts has to follow the invisible slashed grace with a flagged note, and the other part has to be doing anything else, like rests or a quarter note.
This is simple to work around--just change the silent slashed grace notes to silent plain grace notes--and that's what I'm doing. But it might indicate something subtly wrong with the code, so I'm reporting this in case anyone cares.