I have removed the extra entries in mime.info and mime.types. I have changed to:-
$wgFileExtensions = array('png', 'gif', 'jpg', 'jpeg', 'doc', 'xls', 'mpp', 'pdf', 'ppt', 'tiff', 'bmp', 'ps', 'pps');
I've saved the document in Word .doc format and using the markup:-
[[File:AgreementV2.doc]]
Gives me the same error:-
"File extension does not match MIME type."
Charlie
MediaWiki v1.16.0, PHP v5.2.6 and MySQL v5.0.77 Apache v1.3.41