Subwoofer issues

My First day! My first attempt at home theater!
I just finished purchasing most of the equipment needed for a modest home theater. I used the MCACC room  calibration on my Pioneer 1018ah for my 5.1 set up and now the subwoofer isn't performing like it did last week when I purchased it. Now it doesn't turn on or when it does the bass isn't noticable for 80% of the time.  I am using a Martin Logan Abyss through the LFE input. The rest of my system consists of a Samsung 1080p 50" plasma, Pioneer BDP-51FD, Energy RCLCR center, Energy RC10x2(fronts) and Monitor Audio M90 HDx2(rear speakers). I hope I posted this correctly and didn't make anybody mad. I have been reading these forums and thet have been very helpful. Any tips or suggestions would be greatly apreciated.