Try to use the following command line: %rom%
In the daphne.bat file the game name/rom name is mapped to a bat file:
IF %1==Cobra_Command %BATCHPATH%\Cobra_Command.bat %DAPHNE%
So there is no need to send the path or the extension to the daphne.bat. I will also change the command line for daphne in the emulator preset file.