Zotfile not compatible with the Zotero 4.0.3
I assume others have discovered this as well. I wouldn't have updated the new version of Zotero had I known that Zotfile would no longer work.
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Upgrade Storage
http://forums.zotero.org/discussion/5301/13/zotfile-zotero-plugin-to-rename-move-and-attach-pdfs-send-them-to-ipad-extract-pdf-annotations/
As you can see there, 4.0 compatible Zotfile versions are available for download (also, the Zotero upgrade was required for FF20 compatibility - most Firefox users were auto-upgraded to FF20 this week.)