Premiere Pro playback Footage issue - W/ After Effects Composition

Hi, I've had a very irritating issue as of late.
I've been working on a project for the past couple weeks and it has been going well.
I use AVCHD 1080p 29.97fps 24p footage. It plays perfectly fine in my Premiere Pro CS4 and After Effects CS4. I have used After Effects to replace many parts of the footage and has gone very well... Except one piece of footage.
For what ever reason, it plays terribly only when I apply an After Effects composition to it. If it is the raw footage, it's fine. If I alter it in after effects it's fine. But if it's altered from AE and I attempt to play it in Premiere Pro it repeats old frames. A mixture of stuttering and several frames back through out the whole clip.
I have NO idea what caused it or why it's happening.
Does anyone know?
Thank You.

AVCHD footage is highly compressed using a GOP compression scheme. This makes it unsuitable for heavy processing and subject to all kinds of errors and artifacts when re-compressed. The best workflow is to convert (transcode) your AVCHD footage to a lossless or nearly lossless codec that preferably uses YUV color space. I work mostly on a Mac so my preference is Apple ProRez 444. I transcode everything that I work on that is going to require more than just straight cuts.
Try transcoding (Adobe Media Encoder or Compressor or even Quick Time Pro are a few of the options) your problematic clip, replace the AVCHD footage in your AE comp with the transcoded footage, then re-render to a lossless or nearly lossless codec. Bring your new render into PPro and render a preview. Let us know if this fixes your problem.

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You haven't given us much to go on here. What exactly are you doing and what exactly happens when you try? Which specific version of each program are you using? (Go to Help>About...)
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So basically, i want to track a title to a piece of footage, so i've made my ins and outs and my footage is placed on my timeline in premiere with my title over top. Now I select the two pieces in premiere (the title and the clip) and I hit replace with after effects composition, and it ADOBE does it's thing etc.
but now in my AE project window I have two copies of my title file and two copies of my mp4 clip.
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now. if i just delete the two "compositions" that are masquerading as files in my timeline and drag down my mp4 / psd then my tracking becomes available and all is wonderful
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I'm sure you've figured it out.
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Premiere Pro playback Footage issue - W/ After Effects Composition

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