Well it could be a few different things.
1. From my understanding there is an import setting that will adjust tyour images upon importing. (I say it like that because I dont use it, jsut heard abou ***.
2. If you are shooting RAW, make sure you cameras raw processor is up to date for aperture, I had a similiar proble, and when I ran updates and received the RAW update i had no problem
Other than that, that is all I can think of without seeing an example or more info. For example is it jsut one color, jsut certain photos, etc.
Hope this helps as I could be way off as well.