I've made some changes to Special:Upload while fixing up some file overwriting problems ( http://bugzilla.wikipedia.org/548 ). I don't think it should break any upload bots, but please check if you have problems.
The form interface when it asks for user confirmation (eg for overwriting) is slightly different; it runs more of the fields through the session instead of the form.
-- brion vibber (brion @ pobox.com)