It sounds like your TV is telling the player that it can't process a Dolby Digital or DTS bitstream, which is not surprising. Do not set the player to PCM, though. Your TV has no problem getting PCM over the HDMI connection, but you'll also be feeding the 990 a PCM signal over the optical cable, and that means you will lose both Dolby Digital and DTS audio - you'll be feeding the 990 the a downmixed stereo signal stripped down from the Dolby Digital's 5.1 and nothing at all from DTS.

If setting "Screen Messages" to "off" in the player's display menu gets rid of the message permanently, that's probably the best solution. The alternative is to ignore the message.