I don't know how Automatic Duck works exactly, but are you importing it from the same computer? Is the footage all on a network drive or an external drive?
I don't know if you've tried to use the "Replace file" command for one of the files--usually the rest update accordingly.
Here's a script that may help you replace paths if they got messed up somehow:
http://aescripts.com/batch-search-n-replace-paths/
You might want to try this script to import the FCP XML instead of Automatic Duck--it's worked well for me:
http://www.popcornisland.com/2009/03/final-cut-2-after-effects/
Dan Fredley