You might want to update to a more recent version of AutoDomain, we (I) gave up on scriptrunner when even McAfee started flagging it as a possible virus.
The most likely issue though is that scriptrunner is running prior to the script being written?
Does it work if you run it manually post install?
I found the http://sites.google.com/site/ctogonewild/Home/intersting-files collection of files and updated my autodomain.vbs files and switched to autodomain.exe from scriptrunner.exe and it seems to have resolved the issues i'm having.
Ironically, I might have to "reinvent" scriptrunner to get around the fact that Primalscript won't let me package a VBS to run in 32bit mode on 64bit systems. Annoying.. :-(