Are you using 2 channels for music and a full set of surround speakers for movies?
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Too much jitter from the Toslink on the Mac Mini. I would never use it this way for music. Your software choices are probably at fault too.
Consider instead an async USB converter wired with USB cable. S/PDIF coax to drive the DAC or SS decoder. These range from $100-$3500 depending on the level of sound quality you want. USB cables range from $50 to $800. 1.5m S/PDIF cables are $100-$1K. They should be 1.5m long at least. The top of the performance curve requires an expenditure of about $2600.00. This will beat even the best $15-30K CD Transports, so its worth it.
The other problem is likely your playback software and ripping software. iTunes on a PC or Mac does not cut-it. See these guidelines:
Another option just occurred to me. You could continue using the Toslink output from the Mini, but feed it into a reclocker like the Synchro-Mesh and then to your DAC/Surround proc.. This will take care of the hardware jitter. A lot cheaper than a USB converter, and almost as good. Then you just need to take care of the software part of it.
Rezanazari, haven't heard from you yet on the first post, are you using your home theater's sub when listening to music? My AVR has settings that will only use the front speakers if I want, I think it is called "standard" or something. I typically use one of the home theater surround settings for two channel music in my HT, I forget which one, but the processing fakes 5.1 out of a 2 channel signal.
Signal processing makes a huge difference when playing two channel on an AVR in a home theater. I had to tweak and tweak and TWEAK to get my Denon AVR to sound as good as a 20 year old Yamaha receiver in 2 channel (front speakers only).