Bass management problems anyone?

It seems my system does not handle bass management correctly. I have been battling this problem for a long time. I confirmed this yesterday. While playing a stereo cd with the settings on my anthem pre/pro set to mains-large, surrounds-large, subwoofer-yes I got no sub output at all and it sounded very thin and nonmusical. I changed the rears to none and the bass was there and the music in its entirety sounded beautiful. I had the anthem effect set to stereo to play in 2 channel mode. It seems there is no rhyme or reason to this. I can lose the bass with speakers set to small, subwoofer yes sometimes also. Sometimes it comes in while just sitting there listening or toggling the speaker settings. I never know what to expect. Here today, gone tomorrow. Has anyone else had a similar problem? Thanks, Tim