[Matt Reinbold]

Just another solution in case the above didn’t fix the problem. I had the same issue above, even after converting the .eps to RGB under File >>> Document Color Mode.

I found the crux of my issue. When saving your .eps, there is a tick mark, that may be automatically selected based on the project, that says “Include CMYK PostScript in RGB Files.” Turning this off, in addition to changing the the document Color Mode, should fix nagging issues of a file’s colors importing incorrectly to After Effects.