What is the OS and Version of the product?
What are the Project settings that you have used?
The change is visible on different monitors/Multiple machines or on the same one?
What color workspace/Profile has been used?
Have you used display color management option?
OS X 10.8.5
After effect CS6 version 188.8.131.52
The change is visible on all monitors, machines and operating systems.
Depth: 16 bits per channel, Working space: Generic RGB Profile.
The Display color management option is checked on all projects.
But on one of them the Linearized Working Space was unchecked. Looks like that might fix it.
I will suggest you to turn off the Display Color Management option or make sure that all the display devices are caliberated to same color management and then check the difference.