This reminds me of an issue where I uploaded new vbulletin files over existing ones multiple times but I was still having this issue... it turns out, my ftp program did something screwy and didn't really overwrite them even though I clicked yes to all. So in the meantime, if it helps, try downloading a few of those files and opening them up to see what the version # is (or check them via the browser if your server has remote file management).
Hope this helps in the meantime.
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