I was struggling to intall SG Vault alongside SharePoint Portal 2003 and tried to follow your official help reference:
http://support.sourcegear.com/viewtopic.php?t=3147
Since I'm running my tool in a locked down environment with only a single public IP and a single public port (80), the new website approach was not doable.
Luckily, I ran into almost the exact same problem a few months ago when trying to run a Web Service alongside SharePoint. The Microsoft-recommended solution for running ASP.NET web apps alongside SharePoint is here:
http://support.microsoft.com/kb/828810
If you follow the steps laid out in that article, the VaultService works! The key, aside from the new web.config settings, was setting the exclude path in the SharePoint Central Administration console. Once I did that, voila, my vault issues were resolved. There's no need to move Vault out of the inetpub folder & no reason to create a new website -- everything is doable using the tools that are already there.
Installing SourceGear Vault Server with SharePoint
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