Just spent a few days writing the build procedures for BizTalk 2006 development PCs.  I created a nice Windows 2K3 base with SQL, Office and Studio all ready for the using.  This was my starting point for the installation of BizTalk 2006.  One of the first steps was to rename the machines and re-SID them with NewSid so we could be good corporate citizens with uniquely ID'd machines.  When it came time to install SharePoint, I chose to do it on a non-default web site and to create unique accounts for the App and Admin app pools.  This would help mirror the eventual production configuration.  Everything seemed to go well and then when the step came to verify the extended SharePoint website - the fun began.

The main issue was that I kep getting 404's when trying to accesss the templatepick.aspx page for the new server.  I kep getting 404's.  I allowed directory browsing and could browse around to my heart's content - all the way up to that file.  Then - 404!!!!  I reviewed the logs and also noted:

"Unable to get the private bytes memory limit for the W3WP process. The ASP.NET cache will be unable to limit its memory use, which may lead to a process restart. Error: 0x80070005".

Very troublesome.  I then reran the install procedure without NewSID and it worked flawlessly.

So.  My solution was to not NewSid.  I did however come accross an article that listed some extenisve steps to make the whole thing work after NewSid does its thing:

http://blogs.interknowlogy.com/billsheldon/archive/2006/05/22/2705.aspx