OK I found out what was wrong...
The code for colorboxes has changed. When did this happen? I went back to the examples page (which has been updated to 3.1 examples---Thank youhttp://wdn.unl.edu/wdn/templates_3.1/examples/
) and found that the code for colorboxes has changed from the old examples. I am not sure why the old code does not work. But this will mean that you need to change the code on your pages for colorboxes.
The script I had references the specific folder for the templates_3.0 so I had to go in and change that to templates_3.1 and then the function worked. So this will need to be another edit that you will need to make when shifting over to v3.1
Question: Are there other content resources that the code must be changed to work in the 3.1 version?