Modify your config.ini file entry to do a:

;@EXEC_ONCE /bin/bash -c "/usr/local/bin/start_empire 12 &"

Note the 12 instead of a 10. This will start Empire after a 12 second delay. The delay is needed to allow the player app time to start up and sieze the IrDA port, just so we can sieze it back. The lines:

start_empire: sleeping for 10 seconds...
player.cpp : 385:empeg-car 2.00 2003/04/01.
start_empire: Starting Empire...
IrDA: Registered device irda0
irlap_driver_rcv(), Unknown frame ef received!
Prolux 4 empeg car - 2.1434 Mar 26 2003
Vcb: 0x4086d000
irlap_driver_rcv(), Unknown frame ef received!
irlap_driver_rcv(), Unknown frame ef received!
irlap_driver_rcv(), Unknown frame ef received!

mean that Empire has not successfully taken control of the IrDA port. The added delay may be the result of your player having to account for so many tracks (unless you also have other software starting up such as telnetd or a VNC server, etc). I have seen this happen before to people with over 15k or so tracks.