Great Advice!
Autosetup can play havoc with subs. Also look for any extra LFE settings that your Yammy might have.

My Denon, for instance, had a second setting (other than the main db setting for the sub) that was meant only to apply to DTS sound tracks. It was set for 10db in the difference and really confused me until I found it. This isn't exactly your issue but just an example of an extra setting that might not be so obvious.

With great power comes Awesome irresponsibility.