Dynamic link confusing two separate AE compositions in PPro from different projects

I am using CS5 Master Collection for Windows 7 (64 bit) on an HP Pro desktop (Intel core 2 duo, 6Gb RAM). The tower has two hard drives installed (no RAID). CS5 is installed on the original C drive along with the OS, but the working files, footage etc are all on the larger, secondary F drive.
I am working on a DVD project consisting of several seperate PPro projects. Each project has been colour corrected in AE using dynamic linking. Recently two of my projects suddenly became mixed up, by which I mean the video (not the audio) from one AE composition in one project has taken the place of another in another project. The clip remains the same length, but the link apears to be referencing the wrong clip during playback. Interestingly, there are two clips on the track above the affected clip that fade out and in at either end, during the dissolves between clips, the correct footage plays. It is only when the clip plays by itself that the problem occurs. The next clip also has the same error, though the problem only occurs for half the clip and then suddenly corrects itself. Just to be clear, All clips have been rendered, there are no more than two video tracks on the sequence, and I have tried replacing the composition from the asset menu (in which the clip plays back correctly), but the problem remains in the sequence.
I hope that descrition is clear enough. My guess is some kind of file path error in the dynamic link, perhaps due to the separate hard drive. But I really wouldn't know. I'm very pressed for time right now and I'd prefer not to go against workflow and re-edit a new composition in AE, I would also like to understand what is going on in case it happens again.
Any help with ths problem would be appreciated,
J

Thanks Colin, I tried what you suggested with both the AE Project that it should be referencing and the AE project it is erroneously referencing but both failed to fix the issue. Its as if a hidden clip were laid over the top of the one I want to play. Frustrating.
Date: Mon, 24 Oct 2011 19:47:03 -0600
From: [email protected]
To: [email protected]
Subject: Dynamic link confusing two separate AE compositions in PPro from different projects
    Re: Dynamic link confusing two separate AE compositions in PPro from different projects
    created by Colin Brougham in Premiere Pro CS5 & CS5.5 - View the full discussion
It's not the comps that are the problem; it's the project file names themselves. You can have all the comps in a project named the same thing, and it'll be fine, but naming projects incrementally is an issue. After Effects includes a versioning function (Save and Increment) that will create a new AE project file with a serial number, e.g. AE Project 01, AE Project 02, etc. This is all well and good if you're just working in After Effects, but Dynamic Link gets confused and will usually start looking at the later project file for comps. That will just create a big mess, as you've found. Changing the names of the project files won't help things relink automatically properly, but it can help you fix things. Make all your DL AE comps offline in your Pr projects, and name your AE projects in a manner that is not serial (give them more random names). Select your offline AE comps, and right-click > Link Media, and point to the new AE project. Things should link up correctly then--but if they don't, you'll just have to remove all the AE comps from your Pr project, reimport the comps from the newly-named AE project, and replace them. It's a pain but it'll probably just keep getting worse if you don't.
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