Just a quick example from a current project. It isn't perl specific, but as I said above, it is usually IIS.

I developed a web app using Visual Studio on Win XP/IIS5. It worked great, and passed initial QA for alpha testing. When I migrated it to the test server running Server 2003/IIS6, it failed with an error message that looked like an AD issue. After much digging and debugging, I found out that the default permissions on one of the IIS metabase keys changed from IIS5 to IIS6, so I couldn't read a value that I needed. I had to actually change the metabase key permissions when the software was installed. So much for an xcopy deployment.

Just one of many interesting encounters I have had with IIS in the last year in this position.