Hi,
which DAW are you using?
When you are using the plugin, don't you have it set to Follow Host?
Are you using your DAW as a tape recorder only without setting Tempo?
You must be able to set Global Tempo and Time signature changes, right?
Depending on which DAW you are using, if you drag and drop a MIDI file with Tempo and/or Time sig changes may mess up your audio alignment if you haven't got this set.
BR,
John