Beside wondering what's wrong with the way Firefox saves bookmarks, I am, also, wondering how you are trying to find a bookmark (favorites) in IE.
If you do Bookmark this page in Firefox, you have a chance to select a folder to put it in, or leave it at the bottom of the pile. You get a similar choice in IE7, ui.e. Favorites|Add to favorite, or Organize Favorites, which gives you a chance of placing unattached favorites, in convenient folders. Other than the name, Bookmarks for Firefox, and Favorites for IE7, there is no difference in the way they are handled. It is up to the individual to place the bookmarks/favorites in folders for easier retrieval.
UserAgent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:188.8.131.52) Gecko/2008092417 Firefox/3.0.3
A minority may be right, and a majority is always wrong
~ Henrik Ibsen
WinXP, SP3, 512 MB, SM2.17.1, FF21, TB17.O.5, IE8.0, Google Chrome 26, Ghostwall , Kingsoft5.6, JRE1.7_21.