Software Deployment

I have a software package whereas the files are kept outside of the .MSI. So I have a c:\program files\appdir with a bunch of files in it. Let's call these files 1.txt, 2.txt, 3.txt, 4.txt., 5.txt, 12345.txt just to keep things simple.

Inside the .msi, I am installing only files 1.txt, 2.txt, 5.txt, and 12345.txt. These are all going to the c:\program files\appdir directory. Now when I install the .msi, the only files in the file table are, 1.txt, 2.txt, 5.txt, and 12345.txt. What should I see after an installation within my c:\program files\appdir? I have purposely left files 3.txt and 4.txt out of the .msi but left them in the sourcedir.

What is currently happening is this. I install an application and it seems to copy ALL sources files into c:\program files\appdir. The app is then uninstalled. When we re-install the application, those files are no longer being copied to the appdir. What is going on here?!?!?!!... Been driving me nuts.