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.
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
Waiting for fix in a future release.