CMYK to RGB - Simple issue

Normally CMYK-based artwork translates into RGB fairly easily since RGB has a significantly wider color gamut range. HOWEVER, if the artwork contains any unusual fills or effects the colors can shift dramatically. Transparency blending modes in artwork are a major stumbling block. If objects have varying levels of transparency and the blending mode is something other than normal (such as screen, multiply, overlay, etc) the colors will shift seriously when transferred from one color model like CMYK to another color model like RGB.

It's likely the original CMYK artwork will need to be pasted into a RGB-based Illustrator document. The fills would have to be adjusted as best as possible before placing it into After Effects. The process may be do-able. It's not as bad as trying to take RGB-based Illustrator artwork with lots of transparency effects and moving it into a CMYK document.

The difference between CMYK and RGB color is actually quite simple. CMYK which is used for print jobs is basically a mix of 4 colors which are used as ink on a press: Cyan (a shade of Blue), Magenta (a purplish red), Yellow and Black (designated as "K" to avoid confusion with blue). By overlaying these colors in different percentages the appearance of full color can be achieved.  RGB color is a color based on light represented by the pixels used on a computer screen. This color space provides a much wider range of colors many of which cannot be accurately represented in CMYK. RGB colors that are not achievable with CMYK are referred to as "out of gamut". The problem that you're having with certain converted colors looking better than others when switching between the two modes is really a matter of luck of the draw in terms of the actual colors being used. Certain CMYK colors that are within gamut may appear closer to their original look than others when converted to RGB. Others will look wildly different. Usually questions like this will bring up instances of original RGB jobs looking dull when converted to CMYK. Your experience shows that the issue exists in either direction of color conversion.

What are your color profiles being used? It's odd since most of the CMYK color range exists in even the smallest RGB profile. What happens if you rasterize the file in Photoshop and convert there?