I often get logos as vector files in CMYK. Converting to RGB in After Effects or Photoshop (or even Illustrator), I lose blacks in particular, and contrast in general. Typically I pull the levels in Photoshop, or swap to black in Illustrator, but is there a particular setup I could change in my color settings to avoid the trouble?
open your vector logo in illustrator
File > Document Color Mode > RGB
Select Your Logo
Edit > Edit Colors > Convert to RGB
If You have an older version of illustrator, I believe convert to colors was in the filter menu.
This should fix it. If illustrator making he colors look different than in your video program, turn color management off in illustrator. In worst case manually change the RGB values in Illustrator as your vector shapes are in RGB now.