Yeah the gain setting at half way for the sub is just a very general recommendation but sub amps vary quite a bit. For most of the commercial plate amp subs I've used, it's usually more in the 1/4 or 1/3 setting using Audyssey setup to get the sub in a good range (as long as the setting after Audyssey is better than -12dB, anywhere else in the negative range is usually fine unless the auto-on circuit of the sub won't work with it, but that doesn't seem an issue in your case since you had it set at -12 already).
Thanks for the update on your master volume being at -12 dB rather than 12 dB....HUGE difference to your speakers particularly