Hmm, that is strange. Is the site working ok besides the setup page saying that?
Are you sure you upploaded all the files with no errors? Sometimes I find it works better if you don't upload them all at once. Some of the big folders I ususally upload o0ne at a time, like the Setup , ClientScript, Data folders.
I would have a look in the mp_SchemaVersion table and see what versions are reported there.
I would also look in the mp_SchemaScriptHistory table and see if any of the scripts logged errors.
Hope it helps,
Joe