How are you hooking it up? There are two optical and 1 RCA audio inputs on the HT system.
You might not have the proper source selected on the HT. If you're sure you have the proper input setting selected, then you should be getting audio.
What kind of files are you having trouble with?
I have a samsung ln52b750 tv and a samsung HT-BD1250 home theater system. I have downloaded the PC manager softare to my PC and I am able to access and play the content. However, I am not getting any sound output from the hometheater speakers when doing this. The only way I am able to get sound is if I turn off the external speakers from the menu and use the tv speakers. Is there a way to have the sound come through the home theater speakers? Thanks in advance.