No site objects when attempting to collect from ISA (2004) machines using pre-installed agent, especially when the following MS hardening template http://www.microsoft.com/technet/isa/2004/plan/securityhardeningguide.mspx has been implemented.
This occurs because the filters and the data sources need access to certain services that are disabled when the template above is applied.
WORKAROUND:
1. Make sure the Remote Procedure Call (RPC) Locator and Remote Registry services are both in a 'Manual' instead of 'Disabled' state on the ISA server.
2. Remove the filters from both the site and gathering policy by right-clicking on each, going to the Filters tab and removing the MS ISA filter
STATUS:
Waiting for fix in a future release.