To improve your setup reliability the following should be done:
Decide which setup tool you will use: Wise, InstallShield, WiX, or another brand.
Track all files in your product in a spreadsheet or, better yet, a database. If you are using WiX, the files are listed in the .wxs file.
Build setup every day, and practice deploying your product to test machines every day. Do not release the build until setup has been created successfully.
Follow the example in Figure 13.1.
Start pushing the setup responsibility back to the developers who own the modules.
Read Rob Mensching's paper, "Using the WiX Toolset to Integrate Setup into Your Development Process," which is located at http://msdn.microsoft.com/library/default.asp?url=/library/en-us/dnwingen/html/wixsetup.asp.