It is probably the Windows security feature known as User Interface Privelage Isolation. This is where a lower integrity process is not allowed to communicate with a higher integrity process.
This was added to Windows Vista to prevent what's known as a Shatter Attack.
The security concern is that a malicious application can try to communicate with an elevated MatLab process, possibly using it to write to secure locations.
For example, your C# application is attempting to use MatLab in order to save files on the hard drive.