Hi and welcome to Beoworld!
The BS9000 may be in A.OPT 0, where it will not respond to IR commands.
To resolve this:
Turn to standby/off.
On the Beo4, press the POWER button and LIST together. Then press LIST until OPTION is shown, press GO (centre button), and then press LIST to show A.OPT. Then press 1. The power light on the BS9000 may blink to show that it has been accepted.
Remote control should then work.
EDIT: By the way, A.OPT 0 is automatically selected if no speakers are connected to the BS9000