The Problem:
Recently, I ran across a situation where we have an ASP.NET 1.1 app that we were installing onto a machine with the 2.0 .NET Framework already installed.
When the virtual directory was created by the install, all the "non-application specific" file extensions were mapped to the 2.0 isapi.dll file. However, the "application specific" ones were mapped to the 1.1 isapi.dll. So, when I tried to hit the site the first time, a lot of stuff was screwed up. Going into IIS and remapping everything to ASPNET 1.1 seemed to fix everything.
The Solution:
We need to specifically configure the application mappings for the virtual directories via the 'Virtual Directory' tab of the virtual directory in the InstallShield project. We just need to point to the old dll. The behavior should be very similar with the InstallShield project since they mimic the IIS manager.
Windows IIS manager:
InstallShield IIS view:
So, we can just configure the InstallShield project to specifically point to the 1.1 dll's.
Please note that you can't configure existing virtual directories, just new virtual directories.