Because they are listed twice in your Favorites. They would not be there for any other reason.
You can check this out 1 of 2 ways.
1. Open IE and click Favoprites>Organize Favorites
2. Go to C:\Documents & Settings\<username>\Favorites for XP
C:\Users\<username>\Favorites for Vista and Win7
There you will see your favorites listed. There you can add more if you created a shortcut to the webpage on your desktop, you can remove favorites, you can modify the layout by moving some to the Link bar or removing them from there. that is the main source for the IE Favorites. You can just copy this folder if you wish. then just copy it back.