Problem: When installing ArcIMS, the permissions for the Web site and output virtual directories are reset back to default
After installing and configuring a new version of ArcIMS, the customized settings for the already existing Web site and output virtual directories in Internet Information Services (IIS) are reset back to the default.
This is a known limitation. The ArcIMS postinstallation configures the virtual directories in IIS with the default permissions and settings.
Solution or Workaround
Manually reset the permissions to the preferred custom settings in IIS after upgrading.