Hard to say without seeing the project, but two possibilities come to mind, (which you may or may not have already thought of).
1) If you’re rendering one with an alpha and one without, and you’re comp has a black background, it could be that the black BG is mixing with the image when you drop the alpha channel. If you were to then put the alpha’ed one over a white BG, or maybe just disregard the alpha completely, it would appear brighter.
2) Going between an editor like FCP and AE can cause issues, because AE usually renders in RGB and most editors render in YUV. The shift in colour space can cause a drop in brightness. Also, some codecs use YUV and some use RGB. It could mean you need to check your source files, AE project, output codec or editor timeline to see if they’re all the same.
Hope this helps.
Tristan