Check your color managemnt options in PS and AE. The files are possibly tagged with a specific profile that may act differently across versions.
My color management settings are "Syncronized: Your Creative Suite applications are synchronized using the same color settings for consistent color management." Perhaps this could be a problem if it is different from CS4? Is there a way to "Desynchronize" it perhaps?
Just turn color management off. You will still have to do things like preserve the legacy Gamma in the output and carefully choose your production and delivery codecs to maintain consistent color.
In Bridge, my color settings are shown as synchronized (some kind of universal deal I guess), but the Photoshop files and the After Effects file are not color managed. What is confusing me is how completely "not color managed" files can interpret RGB values for anything different than their face value?
My Workaround (Not a Solution):
In light of how specific this problem is, I've decided to simply match the Photoshop files to the After Effects footage with a gamma adjustment using a levels effect. For this situation settings the levels to .88 corrected the problem. However, exporting the project from Premiere results in a darker movie file than the orginal so I was forced to correct the gamma on the export as well. The new export (after the corrections) looks less appealing to me but as a standalone product is acceptable.