This is a pathological case, but causes cryptic, poorly reported failure. If $wgFileExtensions contains a value in common with $wgFileBlacklist, UploadWizard refuses to upload files of any type.
This happens because Setup.php executes
$wgFileExtensions = array_diff ( $wgFileExtensions, $wgFileBlacklist );
To fix this, either Setup.php should use array_values( array_diff( ... ) ), or else UploadWizard.config.php should say
'fileExtensions' => array_values($wgFileExtensions),