MIDI and audio out of sync?

Apr 5, 2008
544
0
16
Washington
This guy I'm recording tracked some keyboards, and I decided to record a MIDI file while we were tracking the audio just in case he was sloppy and I needed to quantize some stuff (he was). Apparently I didn't check this at first, but the audio and MIDI tracks don't line up with each other. I ended up messing with the tempo before I had noticed this (I had to align the Pro Tools tempo with the drum machine track that he used as a metronome so I could quantize the MIDI), but I don't think that would cause the MIDI file to conform to the new tempo or anything like that. What could be causing the MIDI track to be off?