No-rez installed.

You're getting good advice from MLundy. But these two readings are drastically different. It looks like you turned up the volume of your subwoofer or changed the mic position. The previous reading, where the 20Hz-200Hz region was flatter, looked much better. I doubt that No-Rez would have changed that. Did something else change? This reading has a huge peak at 50Hz and the other one is flatter, but seems to have a lot less around 35Hz and below.
Also, are you crossing over the main speakers to cut out the bass? It looks to me like it would be useful to lower that frequency if you are.
But these readings seem to have the subwoofer and main speakers more in phase, which means that we're getting closer.