Ok, so for the latest, I've been on the road, and away from my studio.
I had the hard drive replaced, and I am still having the same issues. I have discovered that if I completely skip the Saffire, using the built in microphone and speakers, it will record in time. If I use the saffire either input, output, or both I get the recording late on playback. I have reset all settings back to factory on both the Saffire and in Logic. I have restarted the Saffire and the Mac.
Any ideas?