What is it about those two emulators that makes them so special? Is it an uncommon mapper arrangement that isn't handled very well in other emus?
I'm the one that did the expansion for DOAE ROMs. Maybe we're not doing something right when we expand but here's what we do:
1. Back up the ROM.
2. Open your hex editor and expand the ROM to 80010 bytes. (ie...add 0's to the end until the last byte is 80010).
3. Copy all the data that currently exists at $3C010-$40010... and paste it to $7C010-$80010 (this is the "master" code of the game, for lack of a better term. It must stay at the end of the ROM).
4. Change offset $00004 from $10 to $20 (to show that you've doubled the size).
Now you have a 512k ROM.
It seems only certain emulators (like FCE Ultra) read the extra ROM pages when using this method.