Hello and welcome to Advanced Installer forums,
Indeed, this happens because, at install time, by default the registry permissions are set earlier than the IIS web site installation. As a workaround you can proceed like this:
1. go to "Files and Folders" page and in the
"Permissions" tab of your folder enable the "Keep existing permissions" flag
2. go to "Table Editor" page and select the "InstallExecuteSequence" table
3. edit the "Sequence" field of the "AI_ConfigPermissions" action so it be scheduled after the "AI_IIsInstall" action (for instance set it to 6550)
4. rebuild and test the installation
Please note that our "Table Editor" feature is available only starting with the "Enterprise" edition of Advanced Installer.
Let us know if this helped.
All the best,
Daniel