If I understand correctly,
When you load Rockets + Mk82SE + Mk82, you don't see the Mk82SE.
Then, same loadout without Rockets, i.e. Mk82 + Mk82SE, you can see the Mk82SE.
The problem here doesn't seem to be the mix of weapons, it seems that adding the rockets makes the SE not visible.
Can you specifiy exactly which pylons you're using for both?