Honestly, I'm surprised the 003 works with anything other than PT in 10.6.2 at all. I'm sure DIGI does not have 64 bit drivers for core audio. They are usually a good 6 months behind the curve with things like that... if at all.
That config works fine for me both in 32 and 64 bit mode so not sure what is going on with your system. All the versions seem to share the same preferences. Actually now that I think about it, the audio unit scanner only works in 32 bit mode. So if you add a new AU you'll need to boot in 32, scan the AU's and then reboot in 64bit mode for them to show up. However this is not the case, on my rig, with the 003r. but maybe could help?
good luck, j
Also - forgot to mention my experiences with this...
Selecting the 003r as the System Output in the Audio Midi Setup was causing Logic to crash - not exactly sure why - I'm sure someone here could probably explain that better than me. But when I switched back to "Built in Output" Everything behaved as expected.
Also a warning for anyone here using Pro Tools 8.0.3 - there is a bug that causes random white noise bursts that could causes damage to equipment (including your ears!) and most recommend going back to 8.0.1 - check the DUC and you'll see plenty...
Are you using your 003r as your sound card for Logic? Also, didn't you just say that you'd upgraded to PT 8.0.3 and that everything was fine but that 8.0.3 causes random bursts of white noise?
Just wondering because I'm about to install Snow Leopard on my backup drive. I have a 003r for ProTools and an RME Multiface for Logic.