Similar to this, I've installed 2.5 on my site and I'm using the FCKeditor in an attempt to give my users some kind of rich text experience.
The issue is this, newlines, paragraphs work fine when I edit them from firefox.
Internet Explorer however exhibits some weird behavior, It accepts the 1st draft fine but then on every save thereafter strips out on more
or <p> tag. All the while the front end completely ignores the markup and presents one solid chunk.
And the TinyMCE is a no go too. (as is suggesting to my non-techie users to use the non-visual editor).
I like wordpress a lot, Have used it on multiple sites but for every one this has been a repeated issue and I've yet to see a good reason why these markup tags _have_ to be stripped out.