Craig,
The custom properties defined for all the Orions should be collected by EOC when it polls for its data. Let's start by verifying that EOC has polled the Orion in question. In the EOC web console, go to the "Orion Servers" tab. See if there is a date/time under the "Last Polled" column. If there is, then let's open the EOC database and verify that in the "EOC_NodeCustomProperties" table, there are custom properties for the site build and responsibilty. These columns should be showing up in the that table. If they are not, are the default custom properties (City, Comments, or Department) showing up as columns here? (Assuming that you haven't removed them from the nodes using the "Custom Property Editor")
I'm not sure what filters that you are talking about. Can you explain a bit more or better yet provide a screenshot of these filters? Further a screenshot of the SWQL reference would be helpful as well.
Thanks,David