Which version of AdvanceMap are you using? If you are inserting new maps, I'd have to recommend 1.95 over 1.92 for that specific purpose, as long as "AdvanceMap.INI" has been edited to use the right free space in Emerald. If you are already using 1.95, I think changing the .INI a little should help.
Here's the relevant part of mine, with the highlighted areas to show changes:
Code:
[Version:BPE]
mainfile=ini/Main.ini
mapsfile=ini/Maps.ini
TilesetIni=ini/EmTilesets.ini
Tilesethoehe=32
Teil1Bloecke=$200
SpriteAnz=253
SpritePalettenAnz=27
AnzMapNamen=213
AnzTilesets=74
SuchByte=[COLOR="lime"][B]$FF[/B][/COLOR]
SuchBeginn=[COLOR="Lime"][B]$9C0B20[/B][/COLOR]
AnzItems=376
AnzAttack=354
"$9C0B20" above may instead need to be "$E3CF64" depending on where your free space begins. My ROM has been through my 'Stabilization' tutorial, so my changes wouldn't apply to a vanilla one, for example.
A-Map 1.92 appears to not always consult the .INI file when it comes to using free space and has corrupted stuff for me in the past because of that, but so far I have successfully inserted several maps with 1.95 after these changes and have seen no glitches so far. Hopefully this helps solve the issue.