Those settings are always correct in the web.config file that ships with mojoPortal. Whenever I upgrade the editors I always change those setings to match so if you use the correct web.config for the version of mojoPortal and you install all the files included with mojoPortal it should be correct.
mojoPortal 2.3.7.0 shipped with CKeditor 3.6.2 and Tiny MCE 3.4.5 and it was listed correctly in Web.config so it sounds like you kept your old Web.config
Still when a site is upgraded there is nothing that deletes older versions of the editors so if the old files are still on disk you could still use an older version of the editor.
Hope that helps,
Joe