Script module error when upgrading to 3.5

When I converted a project from 2.0 to 3.5 today, I got an error that appears from the Web.config.

"The entry 'ScriptModule' has already been added"

It made me think that the cause of the error could be an incompatibility between the old project and the new framework. The problem however only occurs in the server while it compiles fine in my local machine. My initial guess was the server's installation of the framework was the culprit, but after doing some research, I was able to come up with a solution.

For some odd reason, the upgrade wizard that converts to 3.5 adds an extra line of script module in the web.config which duplicates the entry. I was able to fix this by commenting out the line where the error was pointing.