Ditto with my system comparing FLAC and AIFF files through a Squeezebox ... no significant differences, though if pressed I may even say FLAC had the edge. I wonder if the fact that the Squeezebox handles the conversion natively, rather than at the computer end, has something to do with its ability to handle FLAC. Perhaps it does a better job of decompressing the FLAC files and outputting less jitter as opposed to what the computer does, and without worries about sound card, player software and driver variables. It is also well isolated from the nasties inside the computer being networked either wirelessly or via ethernet.
I have also compared the FLAC files via Squeezebox with the original CD, both going through my Cary 306/200. CDs routinely have a minor edge, sounding a bit more open and smooth with better bass. I would venture a guess that this is due to the SPDIF interface between the SB3 and Cary, while CDs are handled directly inside the Cary. But the difference was not significant enough to give up the convenience of the Squeezebox... I love the ability to easily access, randomize and jump between selections.