Hi.
I updated yesterday the TNet plugin and also extracted the server zip. After that, I got several compiler warnings, that "Application" has no XYZ function. I started to wonder what was happening, as these were simple UnityEngine function which always worked. After an hour or so, I realized that the server class is called "Application" without a namespace (doh!). I simply renamed the class then to TNetApplication and it worked fine.
Could you rename that one or move it into a namespace, so that problem wouldn't reoccur again?