I guess I'm a damn fool, but it's the other way around of what it usually is. I used to build websites. A lot. But I always did it on a shell account using some flavour of UNIX. I used a plain-text editor (JOE) to build my pages, happily ftp'ing and cgi-bin'ing my way around. So I took a break for several years...not intentional, just happened kind of thing. I get back into website building, and for the first time I am confronted with WYSIWYG. I have figured most of it out, but I still usually wind up toggling the HTML so I can "see" what I'm doing, if that makes any sense. I'm used to putting something down and having it stay that way. But this editor, and I have no idea what kind of editor it is, always insists on inserting IFRAMES at the bottom. And the more times I edit it, the more IFRAMES rack up at the bottom. I put in other code that I want there, it's there in the preview, but when it's "published," it's gone. I tried contacting tech support of the hosting company but they weren't helpful at all. What I figured out, I figured out on my own. Can anyone tell me why these IFRAME codes keep appearing at the bottom of my HTML? If I don't clear them out they multiply like bunnies.
I've found this to be true of ALL cases where a CMS or anything else uses a WYSIWYG bar - you have to disable it to be able to get code to behave the way it should! Most of these things are flawed. This goes for Wordpress and many others...
I've never had that happen, but I used to WYSIWYG and now I notepad.exe it. It's good to code, but if Dreamweaver and Microsoft Expression Web have both turned out to be pretty good (better than expected even).
What host / CMS are you using? Try doing a search for "tinymce" or "fckedit" - those are 2 very popular JS wysiwyg editors that end up on cms'es. You may be able to find some config options.