Are you sure you did follow instructions precisely?
Because there are multiple steps required, involving messing with files in C:\Windows\Microsoft.NET\Framework\v2.0.50727\CONFIG directory.
I would suggest to check is it all done according to answer posted by NicholasSiebert.
Anyway, this isn't an error of Movie Battles itself, not even error of Jedi Academy.
The source of the issue is Microsoft .NET, a widely used framework for Windows. You may receive identical error while trying to launch program that aren't related to MBII, so it's recommended to put an effort to fix this issue.