We had the same problem. We ended up having to do GREP search/replace to trim the URL.
We've, unfortunately, had to resort to GRERP s/r functions to get around a LOT of CuteEditor problems.
So, yea, I feel the pain and also feel that CuteEditor needs a lot of polish still.
That said, it DOES have a very nice user interface, which we like, and a decent price.
The reality is that it seems like ALL WYSIWYG editors out there right now have some major drawbacks in one form or another. So, the quest continues for the 'perfect' one.