Why compiled Matlab dll does not stop running in server environment?

I have a Matlab function that reads data from MS Word document. I would like to use it on a server so I created a compiled .Net component from it. The server application can use it when I start it from Visual Studio 2012, but when I try to use it on a deployed IIS 7.0 server it cannot stop running even after hours. The privileges of the calling process are administrator in both case. In every environment the MCR and MS Office installed the same way. Has anyone any idea about the source of this problem?

Thank you!