I had a similiar problem with my 8D.  Here is the thread.

http://www.aperionaudio.com/community/forums/thread/7369.aspx

Long story short the solution for me ended up being a combination of upping the sub dbs and calibrating the speakers using the SPL meter.  It took me a few times and some tinkering with the crossover settings but now it all works great and there is a smooth transition from speakers to sub. 

It does sound like your issue is more centered around music where mine was more movies and TV but hopefully this will help.

Bryan