Another longshot: Toslink or SP/DIF can't handle all the high-tech new sound formats that are part of Bluray. Your Bluray player could be down-converting the newer audio stuff to a traditional Dolby Digital or DTS or whatever. A firmware upgrade could help with that. Alternatively, there might be a Dolby Digital track on the disc which was poorly mastered. You might see if there's some other way to route audio from your Bluray player to your amp (e.g., two channel analog), just to see whether the problem persists. You might also try borrowing a receiver that can suck the high-tech audio bits from the HDMI plug.

(Personally, I'm holding off another year on Bluray, or until my current cheapo DVD player bites the dust. If I went Bluray, I'd also want to get a new receiver, and then I'd probably want to get a subwoofer, and ... I've got other things to worry about right now.)