thats where people go wrong setting up their sound systems, I used to do the same(very long time ago though lol)
turning treble up and bass down to get it to go louder is wrong.
the way I find it easyist to set a system up is to turn the sub off, turn the volume to a good listening level(like where you normally have it) then set it so it sounds good, bass probs about +2/+3 treble usually 0/+1 then add the sub and use the sub settings on the H/U to set that, or via the amp
the rear speakers could be drowning out the bass, or it could be the sub, whats the rear of that model like? with speakers, size does matter, the casing should be thick, strong, and with a big magnet, have a look at the vibe subs and stuff like that in hellfrauds where they have them on display, they have smaller magnets than my components lol
what size is the box? would you say, small/medium/large?
I'd say it was the sub though being a bit weak.
but rock is the hardest to set up imo, with the high treble you get some times can sound harsh, and the many different bass lines can cause the speaker to start to 'fall behind'