I had originally been using the Canvas3DPanel and when that wasn't working and after I looked on the forums for a little bit I discovered the Canvas3DJPanel, but this did not seem to fix the problem, but I didn't really mess around with it. I will try to Popup to see what kind of popups I can create (I haven't really worked with those) to see if they will meet my needs.
Using heavyweight components in conjunction with JInternalFrame does not work correctly. If performance are no problem in your application, you could use JOGL_SWING as OpenGLLayer, so the Canvas3D is also lightweight.
unfortunately performance is a problem with my application and according to this article
http://today.java.net/pub/a/today/2007/08/09/looking-ahead-to-java-7.html it doesn't look like JDK 7 is coming out until 2009.
Thank you both for the help.