(RH9 & FM10) Some internal links don't keep when converting from Framemaker to Robohelp

Sorry. Framemaker and Robohelp newbie here. I'm not 100% sure this is a Robohelp question, it could be a Framemaker question.

I received a Framemaker document and when I convert it to Robohelp some of the internal links transfer and others do not.

Let me show you. My full robohelp document is located here: http://catalog.unco.edu/2011-2012/undergraduate/

If you navigate to Biochemestry, you will notice that under "Courses Offered" the links show up correctly, however if you navigate to English, the Course Links do not work.

Here are screenshots in Framemaker:

Biochemestry:

English:

Is there a setting or a property on these links that I need to update? On the English one, I added <hypertext/> to the format, this put in anchor tags (<a>), but didn't include the href link.

Thank you in advanced!