Well here's a weird one for you. Bookmarks are not stored in the Bookmark.htm file unless you specify it I guess.
Here's a look at my current bookmarks right now. Notice the red circles are two folders default from the browser upon download.
http://www.superporner.com/bookmarks.jpg
Now here is a look at the current Bookmark.htm file in the program files:
http://www.superporner.com/bookmarkfile.jpg
Those two default folders are the only 2 that show up in the Bookmark.htm folder. Notice ESPN.com? I moved that bookmark into the Personal Toolbar Folder and it shows up.
What's the point of having a Bookmark.htm file if it isn't going to store my bookmarks? LOL