Marco,
I don't run the version of AMBEserver installed via the Compass install, but I know you change the port used by AMBEserver with the -p option when starting it. I'd take a look in the startup script in /etc/init.d which launches it at boot time. You can probably add the -p PORT# there and take care of moving it from 2460 to what you want.
For reference, there is a section in my start up script (/etc/init.d/AMBEserver) which looks like this:
case "$1" in
start)
/usr/bin/AMBEserver -i /dev/ttyUSB0
echo "Starting AMBEserver" >&2
exit 0
;;Change it to this for Port 9999
case "$1" in
start)
/usr/bin/AMBEserver -i /dev/ttyUSB0 -p 9999
echo "Starting AMBEserver" >&2
exit 0
;;73,
Kenny, KU7M