I applied a de-noiser effect to back to back tracks on the timeline (CS5 on PC). When the first clip rolled into the second one, the audio was muffled and after a second or so "clicked in" and sounded normal. I had this situation happen everytime a new clip started. It was an interview show with multiple clips back to back.

There is no fade between clips just a simple cut as the interview rolled on through.

Would there be a reason for this?

If I take off the effect, the clips don't do this on playback. I'm playing the overall clip out for ingest into my on-air system.

I just tried it and there's no problem at the edit points, so I can't help with what's happening your end, sorry.

try rendering the audio before playing it out.

Hi. You might also try File/Export/Audio without the effect, then import the whole audio file in and add the effect to it (presuming you are using the effect on the whole track).