Just to add on to the methods above, possibly from another comment on the forums, but the sure-fire way for me to get it to work was:
Play normal regular GBA game
Put Pocket in sleep mode
Take GBA game out
Put in Omega DE
Wake up Pocket
Hit Play Cartridge
Play normal regular GBA game
Put Pocket in sleep mode
Take GBA game out
Put in Omega DE
Wake up Pocket
Hit Play Cartridge