Hi Jon,
In any Altiris reports, the _ResourceGuid (or any column starting with _) is hidden by default, I believe by the ActiveX control that actually renders the report (the ComponentONE FlexGrid control). If you really want to see it, in your query you need to say "Select Column1, column2, _ResourceGuid AS [ResourceGuid]"
The _ResourceGuid is there (if you select * from my_customInv_table in Query Analyzer or SQL Server Mgmt Studio) you'll see the _ResourceGuid column.
Since that column is really just a key that is typically not that important to display, it is hidden. You can use the AS method above if you want to see it. Otherwise, just do:
SELECT vc.Name, custom.Column1, Custom.column2
FROM vComputer vc
JOIN Inv_AeX_My_Custom_Table custom ON vc.Guid = custom._resourceGuid
WHERE vc.[OS Name] LIKE 'Windows%'