I'm not sure I understand your point? It's not new, but we're having a problem, and if we can't recreate it, they can't fix it.
my point is that it's not a new tranny, and you shouldn't be having any issues. i'll take a wild guess and say that if they do re-create it, it'll be considered "normal"
if not, they'll likely tell you you're not pushing the clutch to the ground between shifts, since they can't duplicate (could be the issue...).
another reason i mention that is you might want to see if the 9-3 has the same issue.
so in my eyes it's either an adjustment in the linkage that needs to be made, or the clutch is getting let out before completely in gear...