I know this is old but I just solved a similar problem using CC 2019 versions of both AI and AE.
When creating shapes from vector AI layers in After Effects… the resulting shapes would be a different color even though the hex codes were the same.
If you go into File – Project Settings – COLOR – and uncheck LINEARIZE WORKSPACE ….
the colors will return to normal.
There were absolutely no answers for this anywhere online but now there is.
Cheers.
Animator, Designer, Comedy Writer, Tree Climber, Ufologist