Stupid sanity check: you downloaded the patch files at
http://www.project1999.com/files/P99Files45.zip, correct? I assume so, but it's possible you might have clicked an old link somewhere or something and downloaded the previous patch files (which would cause the behavior you described). Alternatively, if you had old patch file zips lying around in your downloads folder you might have downloaded the newest file, but accidentally opened an old one.
Also (again, I know it's stupid but) are you're sure you're pasting them in to the correct EQ folder? I personally have several EQ installs, so I know it's possible for someone to paste the files in to the wrong one and not realize it.
Other than that my only remaining idea is to do a fresh install.