The only other thing I can think of to try is to see if I can borrow another camcorder from someone on campus that records on MiniDV (maybe a DVX200), record an hour long program, digitize it via FW and see if it gives me the same results. If it does, I'll definitely be stuck. I'm wanting one of those cameras anyway and I'd hate for it to not work either.
I was able to borrow a Panasonic AG-HVX200 camcorder so I recorded a 45 min event w/ clean audio and I digitized it into Media100 via firewire and ...drum roll please...it worked Great! I guess there's just something wrong w/ the way my Canon camcorders (XL-1 and GL-1) record MiniDV footage that Media100 Producer v.11.6.2 doesn't like. I guess I need to pick up an HVX200 now if I'm to make use of these workstations.