What is the difference between running a C# application throw MATLAB .Net interface and running it on a simple .Net runtime environment?

I have a C# application what writes files. If I run simply the exe what is built by Visual Studio, it works fine, but if I call it in MATLAB throw .NET interface, it throws an exception about it can't write a closed stream. I guess there is a difference between the two environment. Does anyone know what is that?