Sorry if I'm insulting your intelligence, but the obvious ones first - the amp is set to optical digital in for that input? - and the movie is DD (not DS which would show as PL)? DD movies are a bit few and far between, so check the info banner carefully.
If these are OK then a bit of a mystery. It must be something going on in the Sony I would think given that the Sky box is set up correctly. Some sky users do report that DD doesn't work for them on some occasions, or they get drop outs etc. Personally DD is always perfect on my box and amp combo (Denon 3803). If you can, borrow an amp from a mate and try it on that.