Codec Not Found error when trying to render/export layered sequence

I have a sequence that I never had problems with in the past but as of yesterday when I open the project and try to render or export. I get the infamous dialogue box saying, "Codec not found. You may be using a compression type without the corresponding hardware card."
I've narrowed it down to only being a problem wherever I have two particular types of media clips layered one on top of the other. In this case it is occurring wherever I have an Apple ProRes 422 (HQ) clip layered with an Animation codec clip containing a graphical bug that was created in After Effects and exported as a Quicktime Movie with RGB+Alpha. Because of the Alpha channel in the bug clip, it is automatically given the Animation codec upon export from After Effects to retain and preserve the transparency needed. I've also narrowed it down to only occurring when all this is combined on a sequence with its compressor set to standard ProRes 422 or ProRes HQ. If I set it to any other codec, such as any DV/DVC Pro or MPEG IMX codec then I can render and export again.
Also interesting is that I can nest the sequence into another sequence and render and export just fine as well, even with it set to either ProRes codec (which will probably prove to be a suitable workaround for the time being), however, any additional insight into this issue that anyone can provide, pertaining to what may have changed or caused my original sequence to suddenly not want to render anymore would be greatly appreciated.
And if anyone else reading this comes across this this same type of problem themselves, then I suggest what I just got to work: Duplicate your sequence, then delete the clips from the new sequence and nest the original sequence into it.
Here is some additional background info if desired:
I'm using FCP 6.0.6. The sequence I have going here is set to Apple ProRes 422 and consists entirely of Quicktime Movie files. Video Track 1 has the main video clips using the ProRes HQ codec (Again, even with the sequence set to ProRes HQ, it doesn't make any difference here). Track 2 has a graphic bug that was created in After Effects and layered over the Track 1 clips at various places. I was able to work with these clips and render as well as export the sequence with no problems last week. However, I was requested to revise the bug in After Effects, and then replace the old bug with new bug and export the sequence again. So yesterday, I simply opened up the After Effects project file for the bug, made the revisions and exported it with a new name using the same settings as the previous bug. The render problem I'm now facing surfaced right when I opened the FCP project file yesterday, before even importing and replacing the old bug with the new bug. I went ahead and imported the new bug and placed it in place of where the old bug occurred. But the render and problem remained. On this particular problem sequence, I can render the new bug if I actually disable or remove the ProRes clip beneath it, but I cannot in turn render the ProRes clip after disabling/removing the Animation clip above it.
Now, I can copy either type of clip into their own sequence allowing the clips' respective native settings (ProRes HQ & Animation) to take effect and then they will playback and export just fine. I can even copy the bug clip (Animation codec) and paste it into the other clip's ProRes HQ sequence and it will render and export just fine from there as long as it is placed next to the other clip and not layered over it. On these newer sequences, it is only when the bug (Animation) clip is layered over the ProRes HQ clip with the sequence set to ProRes or ProRes HQ do I tend to still get the "Codec not found" error.
I've also tried the following steps to try and troubleshoot to no avail:
1. Copied entire sequence into a new sequence. Problem still occurs.
2. Closed FCP, trashed preferences, and restarted FCP. Problem still not resolved.
3. Opened project on another computer, had same problem.

Thanks for sharing these ideas about dealing with this error message.
For what it's worth, I finally managed to solve a similar issue by going into sequence settings, choosing the Video Processing tab, and changing Render 10-bit YUV to Render 8-bit YUV.
Maybe this helps someone?

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