If you mark the "permanent" option, the compiler will embed the Vista-aware manifest into your source executable (means, it makes permanent modifications to your original file). After script compilation, your executable still has this embedded manifest.

If the "Permanent" option is disabled (this is the default and recommended setting), the compiler embeds the Vista-aware manifest only into the file that goes into the installation. It will not touch your original source file!!!

Does this help?

Friedrich