Just a couple ideas off the top of my head. Perhaps the sound difference is due in part to the speakers not being from the same mfr. The reason most people match speakers is for uniform sound. That could certainly be amplifying any geometric problems you may have.

Would it be possible to raise your mains? I haven't checked out JBL's site so I don't know how unwieldy your speakers are. Is it possible to position your center beneath your tv? Is the center above your head when it's on top of tv? Maybe try angling it down at your ear level.