I'm able to import an epub downloaded from AO3 into calibre and then use FFDL update on it successfully. calibre populated with the story URL in 'Ids'.
Can you give me a couple URLs of AO3 stories that have this problem? Or the epubs?
My only thought is it might help you to turn on the 'Search EPUB text for Story URL' option. 2nd from the bottom on FFDL's 'Basic' config tab.