The charts generally have what we used to call an "offset", that is an amount of silence added in front of the audio in order to make it more like an official chart, where the fretboard appears and you still have a couple of seconds before the song actually starts. It also helps to prevent a bug in GH1/2/80s where, if you have a note on the very first beat, the game substitutes a 5-note chord that is unhittable (except by the autoplayer).
Here's some information on syncing songs up, using Feedback and Audacity.
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