There is a bug in the FaceFX.mel script for the Maya plugin of FaceFX 2011. Specifically, the "Batch Export" feature for morph targets only works when the blendshape geometry is still in the scene.
This has been fixed and the available evaluation build has the fix.
If you are using FaceFX Studio, morph target nodes are automatically imported when you open the Ogre content. For plugin-only users, you can re-download the software, or make a one-line change to the MEL script:
Line 322 of FaceFX.mel should read:
string $blendshape_target_array[] = `listAttr -m ($blendshape + ".w")`;