gdg,
Regarding the perceived sound differences between wav and flac, even assuming they are existent, they shouldn't be so significant. Considering that you didn't "need to listen very hard to hear the difference", the problems most likely lie elsewhere. Ok, this reasoning is not proper logic and more like common sense on my part.
For instance, and this might be an obvious proposition, there could be changes in the gain / volume level when transferring from wav to alac.
Also, if you happen to have an USB dac, before conducting any serious sound quality tests on the itunes, I would install usb audio which bypasses all the crappy mixers in Windows. The demo can be found here:
http://www.usb-audio.com. The demo will beep every 30 seconds but you can easily uninstall it later. Also, foobar isn't so difficult to set up; takes about 10-20 min to get it running with Asio.
With regards to the formal argument of "burden of proof", I think a short comparison between two versions of one or two songs using the Ipod isn't enough to establish a substantiated prima facie case for the difference between wav and alac. I realize that a scientific / formal discussion wasn't the purpose of this thread to begin with, but that's probably where all the agitation comes from. I see you have a degree in physics, so I think you will agree that a sample of one or two isn't really saying a lot, especially in light of the strong theoretical background stating the opposite.
In any case, due to the same reasons of ripping all my CDs, I've personally compared wav and alac quite extensively using itunes -> asio (usb-audio) -> microdac -> sr-71 -> Headphile Blacksilver V2 -> Hd 650, and couldn't detect any differences.
In your own interest of saving yourself lots of GBs of storage capacity, I'd just repeat the test under more controlled circumstances, and, as a bonus so to speak, in a way so that the people here can be satisfied as well. ; )