Maybe hard set the url variable in the audit_windows.vbs script and don't bother setting it when you run discover_domain.vbs?
Also, in the Open-AudIT web interface, try this. Go to Menu -> admin -> List Groups and click the "update" icon on the right for the All devices group. Do you know see those computers in that Group?
Have you tried a Domain Audit from the web GUI? This should work as well... Menu -> admin -> Discovery -> Discover active Directory.
FYI - I have recently (as in the last couple of days) done some more work on Discovery to make it a bit more robust. v1.2.2 should be out soon (he says and then takes a month
)