Note: Adding the Base URL will cause a problem for anchor links. Selecting the anchor in your editor will not work.
I fixed the problem by simply adding the location of anchors.
Example:
If your on page
http://www.mysite.com/products/index.html and you select an anchor say #product5 from your editor and save you will get this.
http://www.mysite.com/#product5
so instead of selecting the anchor from the drop down menu of my editor I simply wrote
/products/index.html#product5
I am sure there is a much better way to do this, but from a noob to a noob this is the simplest solution I could come up with.