Why does my audio go out of sync?

I have a project which has been cut up quite a bit. I need to add an audio effect onto the dialogue and so figured instead of adding it to every little bit of audio, I would instead export the audio as an AIFF, bring it back into FCP as one solid track and add the effect to it.

However, when doing this I notice that for some reason the AIFF now is out of sync with the footage? When I export it I get my in and out marks correct. What is going on?