I have found another issue with the anchor tags. Anytime I add an anchor tag with the wysiwyg, it adds it correctly. I can go into html mode and see it and everything is fine. It includes the closing tag and everything. Ex: <a name="test"></a>. However, when I save it, it removes the closing </a> and makes the opening tag end with />. This works with some tags, but IE interprets this as not closing the link. I believe this actually started happening with a recent release, as this was working properly at some point.
We are also seeing a problem with flash movies. It is removing the embed tag from the object randomly, only on postback. It doesn't happen when switching back and forth from wysiwyg view and html view.