Sangeet, are you still tuning in?
I think that there is something to learn from this discussion and the possible misunderstanding between Gene and myself, both generally, and in specific practice on your part.
The topic of sonic differences between amps is an old, tired topic, but one where the newbs, who lack certain baseline knowledge, can fall into the trap of believing that amps can cure certain sonic ills. The whole discussion can lead to misunderstandings that often are largely semantic in nature.
Audioholics is a place dedicated to "the Pursuit of truth in audio/video", so let's establish some facts. All available evidence strongly suggests that amplifiers, should they meet just a few basic criteria, are sonically indistinguishable in bias-controlled listening tests. These criteria are: linear response over the audible band, low noise, low output impedance, and operated within it's power limits (not overdriven/clipped).
Note that that is not the same as the statement "all amps sound the same". An amp, pushing a variable A/C signal (the music, which is actually pretty easy as signals go) into a variable load (the loudspeaker, which is pretty demanding as far as loads go) is as Gene said a complex interaction. It is appreciably different than test signals (very demanding as far as signals go) into a resistor (flat impedance, easy load) as is done in bench tests. The takeaway is that measurements don't tell all, they're just a differential slice, a picture taken from an oblique angle no less, of a larger whole. And unfortunately, as Gene pointed out in regards to the Pioneer ICE modules, not all amps are competently designed to handle the difficult loads.
I should also point out that it is rather difficult to try and diagnose the OP's problems remotely. He has been provided helpful advice, and performed a bit of critical thinking and testing at the dealership on his own, with good results. I'd like to think that we're helping the OP head in the right direction. That direction is looking more and more like an appropriate AVR (or AVR/pre-pro, amp combo) with a clean front end and more suitable for powering his JBLs, which he seems to like well enough. And at least he has the Onkyo to listen to while that is sorted out.