Trouble using audiosnap for MIDI

Hi,
Here's what I'm trying to do to do a full cover of a song:
Imported a real song and somebodies MIDI drum transcription of said song including tempos. Of course the tempos are slightly off, so I wiped it clean and decided to do something I am very familiar with: Creating a click track to the existing audio. Moving through and stating where in Real Time each bar and beat is so that the click will be in time. And with the click and measures in time, so will be the existing drum MIDI. Simple stuff.
 
However, I'm running into something unusual. The MIDI drums seem to be set to Absolute time rather than Musical. But I can select the clip and see it is indeed set to Musical. If I change the tempo to align the click to the audio track, the MIDI notes are no longer on the beat - having stayed exactly where they were before in Real Time.