Thanks for all of the suggestions. I opened up a brand new project and recorded some test audio, which was completely fine, as well as the midi, so brundlefly, I believe you are right...something is amiss in this project. I guess the good news there is that my audio card settings are ok.
After your tips above, I was certain it was a plug-in I'm using called Artillery II, but even after disabling all fx (using the e button), and recording with fx disabled, the same exact amount of offset on a brand new track with no efx going straight to the master bus.
I am actually more puzzled now than before ;)
It is a big project (65 tracks, 15 softsynths, lots of audio), but I'm not seeing any lag and can't imagine this would result in the kind of problem I'm experiencing.