I've never used the Password function of Safari (nor any other browser) so I can't do much testing of the AutoFill prefs capability or reliability. However, I find it usually best to restart an app after making adjustments to its prefs. Sometimes, especially with OS 'owned' apps, a complete cold start.
I suppose you checked/cleared things in the Prefs->AutoFill->Other forms as well as the User names and passwords?
It might help to at least note the 'last modified' date/time on the appropriate Safari plist and see if it is actually making any real changes. Or maybe the username/Library/Safari/AutoFillCorrections.db? Lastly, it might help to Clear History, also. A previously used page may be keeping the AutoFill info even if you've cleared/emptied the browser's cache(s). Utilities like Cocktail or TinkerTool may do a better job at cache cleaning/clearing, also.
I did see a reference to a Disable AutoFill Blacklist Generation in the Debug->Miscellaneous Flags menu. Doesn't seem to 'read' like what you are experiencing, however.