Okay I finally finished transferring all my software over to a brand new minimal installs of Redhat. Everything is working correctly except that when I open the GUI for my program it looks bad. Colors are off, the shadows under buttons are a strange grey, and popup windows are particularly ugly. The GUI was developed on a redhat Linux machine running gnome and looked much better on our dev machines.

Now originally I assumed the problem was I was running XDM, so I installed GDM and changed /etc/initd to start GDM by default like Google told me to. As far as I can tell GDM is now running but the graphics still look the same. I don't know is this is a case that I didn't switch over to GDM correctly and am still displaying the GUI with XDM, or if there is another cause for the poor graphic quality.

Any suggestions on how to fix this or what might be the problem?

What window manager/desktop environment are you using on your "brand new minimal installs of redhat"? What language is the software written in? What widget toolkit does it use? XDM and GDM are 'display managers' - make sure you know what a DM does.