NET Framework 3.5 problems and errors

Hello, I have had some issues with Net Framework 3.5 lately. I installed a Japanese/English game called BVE Trainsim 5 which requires Net Framework 3.5. It works smoothly except for some rather odd error messages when loading some of the Train Routes. The developer says it must be due to Net Framework and I am quite sure I have installed the route files properly. In the Activate Windows...