Don Pachi may better run with MAME 2010, or FBA 2012, than MAME 2003. And, command line, once game is added for MAME 2010, should be /bin/mame2010 For FBA 2012, /bin/fba
Good luck! Let me know if you still have issues. You may also have the incorrect rom set.
When using FBA2012 mod there...