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I posted on the CKE WSIWYG forum to see if anyone there has experienced anything similar.
If at all possible I would like to stay with CKE WSIWYG rather than reverting back to the inserted commands.
If you like the WYSIWYG you can always use that for normal posts but always switch to standard when you edit that one post with the links. I'm not sure this is actually a problem with the CK Editor itself. It may be in vBulletin's code that converts the WYSIWYG html output to bb code for storing in the database. I've worked with both WYSIWYG code and the vBulletin code for translating it and there are things I'm not quite happy with when it comes to line breaks. Personally I much prefer the standard editor but it's fun and challenging to write WYSIWYG code for the other users