[garret]

Hef,
If you are using Delay comp and then recording to a track you must control+apple+click on the delay comp box on the rec track in the mix window to disable protools from turning off delay comp for that track. This turns the writing blue. When you rec enable a track the Delay comp is disabled for that track that is why you are getting different readings. When you disable it then delay comp is always on, on that track so everything should line up correctly.