I also am not sure how to fix that but I encountered a slightly the same problem long ago.
What I did was, (1) open a clean Emerald ROM with A-Map, (2) I viewed the map where I was having trouble with, (3) I went to File>Map>Save Map As... and I saved it, (4) opened my hack once again with A-Map, (5) viewed the map where I was having trouble with, (6) I went to File>Map>Open Map, and I chose the map I saved earlier from the clean ROM, (7) and then I went to File>Map>Insert Map, (8) A-Map asked for an offset, so I gave it a free offset, and presto! My map was fixed...
I am not sure if this method fixes your problem, though.
In any case, it's worth a try, just remember to save a back-up copy of your ROM.