Midi out of synch

[cgirard]

Here's my method:
I make a midi recording from my drum machine, which makes a record of each individual drum on a separate midi channel so I can print individual audio tracks of all my drums later for stereo mix.
I then print a mono audio track of all the drums as a work track for overdubbing audio.
I then go to work recording.
My problem:
I wanted to back up my work which was getting rather bulky. I broke the audio tracks down into separate folders, sized for burning to CD. When finished I put the tracks all back into the original folder. When I opened the session, it would not find the mono drum mix. I went to re-print the drums, and found that the midi was driving the drum machine out of synch. I could never quite match the tempo. Any ideas why the midi would change tempo or has anyone else run into this problem?