From the samsung manual:

HDMI
- If your TV is not compatible with compressed multi-channel formats (Dolby Digital, DTS, MPEG), you should set Digital Audio to PCM.
- If your TV is not compatible with LPCM sampling rates over 48kHz, you should set PCM Down sampling to On.

From what I've read there is no way to disable audio over the HDMI cable, so it looks like you'll have to endure for the time being, unless your TV allows disabling of the messages.

I do wish that CE manufacturers had waited to push HDMI out of the garage until the audio spec was implemented. DVI would have worked just fine for people until then. Perhaps you should convert the signal to DVI and back through the 990?