My guess is you did not use the Web.config file included in the package. You should always use the one that ships with mojoPortal and re-apply any customizations. Or else you have a setting in user.config that is overriding the Web.config setting for CKeditor:BasePath and pointing to a location that does not exist.
mojoPortal 22.214.171.124 for .NET 4 shipped with CKeditor 3.3.2 which is included under /ClientScript/ckeditor332/ and is correctly configured in Web.config
mojoPortal 126.96.36.199 for 3.5 .NET was updated a few days after the initial release of 188.8.131.52 because it needed a new packaging configuration in order to submit it to the web app gallery. It has CKeditor 3.4 and the Web.config it ships with correctly points to /ClientScript/ckeditor34/
So, either you have a setting in user.config that is pointing to an older version that doesn't exist on disk or you did not use the included Web.config.
Hope it helps,