Hello Benedikt and welcome to our forums,
By the looks of it, I am assuming you are trying to apply a patch.
This may happen if when the patch is applied it needs to access a resource from the CAB. Please keep in mind that at install time Windows Installer caches the MSI installation database in the "Windows\installer" folder, but it stripes down the CAB within the MSI (for size reasons). Then, during the repair operation if a resource from the CAB it's required Windows Installer will prompt for original setup installation.
If your target installation setup is an EXE setup, in order to avoid this problem, you can select the "Do not delete extracted MSI and CAB files" option from "Builds" page -> "Bootstrapper Options" section.
Please let me know if this helps!