If you have not had problems before then what is different about this project? If it is just a single layer that is giving you problems selecting the layer and pressing the u key twice will reveal all modified properties so you can check the settings.
Helpful details include AE version and OS version down to the last decimal point, checking to see if your software is up to date, workflow details including details of any specific effects that may be used, the kinds of footage you are working with or the types of files you are importing, what kind of color management you are using, and how you are judging the final product. I recently helped someone that was judging their renders using a media player that threw in a huge color shift that was not really there.
Color management either needs to be off for everything of completely understood and properly utilized. If everything else is normal and you are seeing color shifts in the production workflow then color management is probably fouled up somewhere. If suspect color management problems the easiest thing to do to verify the problem is to render a frame from AE and render a frame from, in this case Premiere Pro, then take both frames into Photoshop and set the blend mode of the top copy to Difference. If the image does not turn completely black then you have a color management problem. If the image does turn completely black then you don't have a problem with the video, you have a problem with the software you are using to play back the film.
I am not intentionally doing any Color Management, but in trying to figure out if it was on and how to turn it off I unchecked the 'Composite in Linear Color' box in the sequence settings, and that has solved my problem. Will that have any unintended consequences elsewhere in my project?
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