I have occasionally seen issues like this in the past with various version of FCKeditor. I think sometimes it happens if the content is already formatted and you select part of it and format it again.
If the problem continues after upgrading, you can switch back to the previous version of FCKeditor, since the files would still exist on disk from previous versions of mojoPortal. You can put this in your user.config:
<add key="FCKeditor:BasePath" value="~/ClientScript/fckeditor264/" />
to make it use the previous version.
Or you might have better luck using TinyMCE.