This advice is from Wonko the Sane (see here). Following it is the only way to ensure that all dependencies are properly referenced so that success can be replicated.
When testing/adding a new application ensure that only the Core file set is used as a base. Create a new base set of Core files for each seperate application being tested by ensuring that only the scripts in the Core section and the End\Unmount Registry script are selected.
Wonko advises against adding anything to the Windows directory unless absolutely necessary. In most cases any dependencies (e.g. .dll files) can be added to a subfolder containing the application. Please carefully document any changes made and restart the process with a clean set of base files for each application being tested.
Wonko also covers a proposed test environment and some applications that can be used to trace dependencies in the thread - specifically here and here.
Please report any successes in the XPSP1 with full commandline and NTFS below 10 MB thread on reboot.pro.
If you see the error message "This application failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem." when running a program it is possibly due to WinSxS dependencies - see here, here and here.