To have the old version recognized just change the version number of the PPU to 2.1.11 and after $ppu->nameConflict and before $ppu->requiredUpload add $ppu->nameToLower = true; this will make it recognize the script and will allow you to reapply the extension.
I have the same or a similar problem. But your hint doesn't helped. In my case there is an error message from Dreamweaver pointing to an error in Pure PHP Upload.htm. It's in german but says something like: the search comments weren't found or are wrong written. Any idea? I even can't insert the plugin on a new page.