FWIW (because I'm not that smart) my very similar set up (Sony receiver) results in 2-channel with a 2-channel source. SPDIF is a digital signal which the receiver decodes. Mine provides a very prominent display indication when it's getting a Dolby signal, and that's the
only time I get 5.1. So my first guess is your receiver has a "feature" whereby a 2-channel signal is converted for 5.1 output. My second guess is you're somehow converting your 2-channel sources to 5.1 before they get to SPDIF. Hmm... I wouldn't have thought that possible unless I was using
AC3Filter. It can "up-mix any audio track (even plain stereo) up to 6 channels." In it's SPDIF settings, however, I've selected "do not encode stereo PCM." So my third (and wildest) guess is you're using AC3Filter (or something like it), and have not configured it the same way as I have.