That's how I configured HGN-733C: LRM20 in left torso, SSRM2 below in external launcher pod, looks cool, I like it.
Nothing promises troubles after configuration saved, weapons located correctly:
But after second loadout configuration, camo spec edit or battle you can see that suddenly all left torso locations are messed:
Issue has quite simple explanation, it's the matter of hardpoints and weapons arrays, I guess that elements of weapons array have no direct assignment to hardpoint location, from my experience it should be very easy to fix.
Actually I have already filed this bug to MWO support, but got an answer, that developers do not rate it as a bug. C'mon, PGI, stop behave like an ostrich and stop calling your mistakes as intended features.
Why am I disturbed by it? Well, it's a part of my MWO fun - to have Mech looks properly. I wonder how many esthetes around, who also annoyed by this stupid bug.