I think that time-alignment is a crock of crap that they're feeding you so you spend more on a cable. Electrons are traveling down a wire like water in a tube. The electrons cannot pass in front of one another, just like the water in the back of the tube can't pass the water in front of it.
And that's way too deep anyway! You don't have "high-freqency waves" and "low frequency waves" in a wire. You have ONE continuous wave that is a superposition of all of them. This ONE wave does not spontaneously split up into different frequencies and somehow force certain electrons to move faster than other electrons.
I don't disagree that your ears heard a difference, but why are they demonstrating these wires in their store? Why don't they come out to your place and use your equipment, as you change the cables back and forth? Obviously, that's not good business, but the point is that this sounds just like a Bose demonstration. That's the kind of demonstration where you can't take your own CD's in and play them, but they have prerecorded music that could very well be altered slightly. Or, how are we to know that all of the equipment remains exactly the same for the two comparisons? Or, getting even more general, maybe it sounds better on their equipment, but maybe it sounds worse on yours.
There are just too many variables in a store-front environment. To really compare them, you should do your own BLIND test at home with several different people listening.
Personally, I believe a wire is a wire. The only thing that they can really improve is the impedence and the quality of the shielding--that is, the amount of signal lost to heat and the amount of interfering noise from external electric fields.
Think about it--if these electrons (which all have a fixed current), still somehow need time-alignment, then you need to go buy a new stereo, too. Your stereo isn't time-aligned. And I bet the windings in your speakers aren't time-aligned. Your speaker cables need to be time-aligned Monster Cables, too. Hell, there are a lot of power sources that use a superpostion of alternating current to achieve square and sawtooth waves. You need new power sources, too!