After two weeks of stuffing around, my home theatre speakers finally work in the manner intended by their manufacturer.
I couldn't work out why they worked fine with DVDs but as soon as I switched to the TV I lost half the speakers. Fiddled around for hours with the various settings but still couldn't get it right. FoL came over tonight and he also stuffed around with it for a couple of hours, trying different settings.
Then, some enlightened hunch made him check the back of the set top box. Sure, everything was plugged in the right spots, but one of the cables wasn't fully clicked into place. One quick click and voila!, we have proper sound.
It was as simple as that.