I managed to fix it by Manually adding an ECU and inserting the tunes from a directory.
1. Start the Miller W.A.R Chip software you got after installing the wizard.(if lost you can get it from here.
http://www.millerperformancecars.com/customer99/wiz/)
2. Find your C:\Documents and Settings\"Computer username"\WC
3. Press tools in the tab of your War Chip software then press Add ECU Type. Then open the ecu file from the WC directory.
4. After that press your first tune tab, then open your tune from the WC directory. then the second and so on.
5. Now you can write your tunes to the Miller chip.(It might want you to select a default tune to do that you can either select a tune then go to tools and then press "Set as default Tune" or you can press CTRL+D.