The master SR A/C drain on the mid 80s 45C is straight back from the pan to the bilge center water trap/drain area at the aft end of the ER.
Believe me when I tell 'ya - there's a LOT of foul smell that will come up through that hose, and that's a negative pressure area, so it'll be sucked up good! Any odor that hugs the floor in the ER will end up in your master SR with the AC unit on.
I put a "trap" in the hose and it mostly fixed this. The other thing to do is clean the coils, pan, and hose out real good on a regular basis.
Finally, under the master SR berth there is an access hatch. The air handler is not sealed from the access areas to those hatches. A bead of caulk around the space where the air handler is (at floor level) to seal the air handler space from the area above those hatches makes a BIG difference - pull the drawers under the berth and lift that hatch going into the bilge - if it stinks down there, and you haven't sealed that air handler's plenum it will suck the fumes up into the AC unit and then into the Master SR!
I fixed all of this on Gigabite and got rid of the smell problems.....
BTW that space (under the master SR) and the companion space on the other side under the galley floor are two of the worst nasty-water traps on the boat. They don't trap MUCH water, but it doesn't take much. They have communication with the bilge in the ER abaft the engines via a tube and once water gets in there it doesn't ALL dry out. Most of it runs out when on plane, but if there's any that can backwash into there, it will - and then sit and STINK. The fix for that is a bit of dishwashing detergent (powder) under those hatches whenver you notice that its all "washed out" - that'll kill the odor and if maintained regularly takes care of it. Also, put some in the forward bilge space under the forward SR floor and in the shower sump - those two spaces also accumulate small amounts of water and go rancid fast, especially the shower sump.
Any rancid water under the floor can communicate smell to the airbox plenum in the master stateroom.....