Ouch! I know what your problem is -at least I think so.
You had a copy of EB installed, but you did not uninstall it before re-installing EB. Apparently the installed doesn't like it that way so it might have "repaired" or "modified" your build.

Thing to do: remove ALL traces of EB install through the control panel (see my guide; it covers uninstalling EB that way); remove ALL traces of RTW that way too (make sure you have a back up first if you have multiple mods installed on the same location as the one where you pointed the RTW (Vanilla) installer to!); then reinstall RTW to the same location; then reinstall EB to your desired folder.

Should update the guide with an explanation of this snag it seems...

But first: lemme know if this worked.