I don't think it's possible to "plasma shield" the IR receiver by software... the trouble is the IR radiation disturbance from the screen, and if the receiver cannot make out the remote control pulses from the noise, there's nothing the software can do about it.
I seem to recall that a hardware upgrade exists for BS9000 Mk.I and Mk.II that makes the IR receiver more immune to plasma screens, already present in Mk.III.
Other than that, I'm afraid the only solution is to relocate your equipment so that the BS9000 won't "see" the screen as directly as it does now. Even a small move might make the difference - if you don't have them both fixed to the wall or something, it might be worth it to experiment a little.