You must be on BizTalk 2010 or newer, so everything should be .NET 4.0. The path that you listed is the only place where the NUnit files are stored. Did you check that the new NUnit that you copied was packaged into the MSI (and that it's a .NET 4.0 version)? You can also look at your <deployment project>\obj\Debug/Release\redist folder to see what files are going into the MSI, and the Output window to see the exact location that everything is copied from.
Thanks,
Tom
Thanks,
Tom