If you're specifically missing the filters, they should be located at /Library/Application Support/ProApps/Internal Plug-Ins/FxPlug/Filters.bundle.
You can copy the FxPlug folder from another Motion 3 installation and put it in this location on the one having the problem, deleted the pref file in your user account just to refresh everything and all filters should show up.
Or, manually download the update package and use pacifist to find the bundle you are missing.