We have been dealing with this issue through email, but I'd like to respond so the public has the same knowledge.
The bug you are running into is http://www.jivesoftware.com/issues/browse/CS-1400. The RTE has been a pain point for us for a while, and we are pushing the date of this bug out to our 2.0 release to allow adequate time to fix many issues related to the RTE.
Just wanted to "me too" running into this bug. It's gotten to be something of a blocker us. My users are reluctant to use clearspace now that this flaw is coming up more and more. They feel like the system is ruining their work, and therefor don't want to invest in it. A quick resolution to this would be very, very appreciated, and may even save my clearspace deployment!
Yep this one is a real pain...not only do we get the new lines issue, but there is an issue with the editor clobbering (basically deleting text) anything in a document that has a [" in it. Seems like an issue with the Wiki macro? Even affects code inside "" tags - basically this test\["somevariable"] in a code block gets clobbered (notice I had to add the '\' escape to even get it to show in this post). Also noticed inconsistencies and formatting issues when you create something in the RTE then switch to text editor and then back to RTE - the formatting gets hosed on bold/italic and bulleted stuff. The sooner the editor in general is fixed (or replaced with something superior) the better. I agree that adoption of Clearspace will be a struggle in my company with the current editor's behavior. Bulletproofing the editor would be a great thing...