Nsgarch- I'll bet (with no risk) that your system sounds like life itself on jazz and acoustic rock- the open quality of the 'stats, plus the plumb the depths foundation added thru woofering. My own experience has, sadly, been less than optimal in mixing wooferinos with my various Quads.
I also agree that getting the stats up off the ground makes a world of difference.
Only question that comes to mind is the effect of the woofer being placed on an equipment stand containing other electronic components- we work like hell to isolate components from all sorts of acoustic, mechanical and self-generated vibrations- have you tried a different arrangement of equipment that doesn't change the relative placement of the woof to the panels?