Logic 9.1.3 Recorded audio out of sync with MIDI and project tempo

I have an iMac 27 with the i7 chip, 8GB memory, 2TB disk, OSX 10.6.7 (just applied), an Apogee Ensemble audio interface, and Logic Pro 9.1.3 running in 64-bit mode. I have just started experiencing this problem. I create MIDI tracks for a software instrument to do some drum tracks. The drum tracks lay down fine and playback fine. I now record a guitar playing along with the drum track. The guitar looks fine while recording, but upon playback, it seems that the guitar is playing back at a totally different tempo than the drums. I do a Detect Tempo on the audio track, and indeed it comes back as a different tempo than the project. I have been recording audio with MIDI for years with Logic. This has NEVER been a problem. I set up the same scenario (same instruments, etc.) in Garage Band and it worked fine. Everything was in sync. Projects I did before this one (all with MIDI and recorded audio) play back fine. Is there some setting I tweeked inadvertently? I'm not positive but I think this started happening when I did the OS upgrade to 10.6.7, but again I'm not sure. Any thoughts on what I can check? The clock settings are all OK, the bit rates and audio format settings are OK. This is a major show-stopper for me. I make my living recording and producing music. Any help is appreciated.