Do you still see Color Finesse applied to your clips, but with reset parameters, or are you getting a "missing effect" instead of Color Finesse?
Color Finesse 3 should read Color Finesse 2.1 settings and update them, but if you were using the older Color Finesse 1.x, then that was considered a different effect and won't get translated by CF 3.
One way to bring the settings forward would be to install CS3 and the older version of Color Finesse on your system (I have CS3-CS5.5 installed on my Win7 64 system), then step through each clip that has Color Finesse applied and do a Save Settings. The saved settings files can then be reloaded into Color Finesse 3 running under AE CS5.5.
Bob Currier
Synthetic Aperture