Oh wow..I just realized how long it has been since i set that up.
executable $HOME/home/battlecat/Downloads/daphne/.daphne
Make it this
executable $HOME/home/battlecat/Downloads/daphne/./daphne
Thus
/.daphne becomes /./daphne (I know it looks strange just trust me here)
also you might want to check your path to your framefiles. You have it set up when used from the "gui" but from from the command line (thus from AM) it doesn't work that way. Make sure the path to your framefiles is right in your AM config! (took me an hour figure that out

)
also
args lair vldp -framefile $HOME/battlecat/Downloads/daphne/framefile/lair.txt -blank_searches -min_seek_delay 1000 -seek_frames_per_ms 20 -homedir $HOME/battlecat/Downloads/daphne.daphne -bank 0 11111001 -bank 1 00100111 -sound_buffer 2048 -fullscreen -x 640 -y 480
remove the $HOME make it /home/ ($HOME means /home/username..so you have /home/battlecat/home/battlecat.Downloads/... to linux/mac)
I'll point out the the default daphane configuration works...however it does have its problems with some games using it. That is why I made every game a separate "emulator"
post back and let me know