Scene 1 Shot 3 - Almost Finished from Sarah Gillespie on Vimeo.
What file format are you outputting from Maya? What kind of passes are you using?
I output them as TIFFs from Maya into Composite in order to composite the layers and had no problems there - it's only when I output them as OpenEXRs from Composite into After Effects then they go really pale. I'm considering just skipping After Effects and trying to put them all into Final Cut Pro instead.