I don't use Bravia Sync on any of my equipment so can't give much help on that. No idea why the amp would automatically switch on muting either when you power it up.
I haven't used a Virgin HD box, but if its like Sky+HD it may tell you in the programme info banner/EPG. Not all HD channels broadcast in HD 100% of the time. Channels like Channel 4 HD & ITV HD only show their respective HD channel logo in the corner of the screen when the current programme is being broadcast in HD, which is a fairly good indicator. You should of course also be able to see the difference in picture quality if it is in fact HD!
The auto calibration is often a good starting point, but usually you get better results tweaking the settings further. One thing to pay particular attention to is the crossover frequency setup. Your surround speakers will only handle bass down to a certain level. You can input this frequency to the receiver, and it will re-direct any audio frequencies lower than this to the subwoofer for playback instead. If you don't set this up correctly you may 'lose' certain audio frequencies.
To set this up correctly go to the back of the subwoofer. It should have two dials on it. Set the 'crossover' dial to max (i.e. all the way clockwise), and the level to just under the halfway point. Next go into the receiver setup and look at the speaker setup section. You should have these particular speakers set to small, which you've done already. Also in here, go and change the speaker crossover frequency for all speakers (they're separated into 'front', 'centre' & 'rear'). 80Hz is normally a good starting point, but these speakers are quite small & according to the manual only handle down to 140Hz. To start with then I'd go for a crossover frequency of about 150Hz.
Once you've done this, you need to check that the speaker levels are set correctly. Turn on the speaker test tone from the 'level' section of the menu and sit at your normal viewing position. If one speaker seems louder or quieter than the others (for example one could be quieter if its sitting at a far off corner in the room) then adjust it accordingly from this same sub-section of the receiver setup menu. Once you're happy turn off the test tone and that should be it set. Try playing a movie with 5.1 audio after doing this and see if you notice any difference.
To give the bass a bit of a boost you can use the bass/treble equalizer on the amp. You could also turn the level dial up on the subwoofer itself slightly, but I wouldn't change it too far from the setting you chose when setting up the speaker levels as described above.
The 'BD Audio Setting' on the Blu-ray player is set at 'Mix' by default. When set at this, the Blu-ray player will decode all audio on board then output it as multi-channel linear PCM to the receiver for playback. Change it to 'Direct' and the Blu-ray player should instead bitstream the audio out to the receiver for decoding and playback. There shouldn't be any difference in what you hear from the speakers, but this should give you the Dolby TrueHD and DTS-HD Master Audio indicators lighting up on the receiver.
Hopefully, you're able to divulge all of that
