Yes, the MTd switch means you are compiling your project with MultiThreaded Debug libraries, GDK needs to be compiled with plain MultiThreaded libraries, you can change that option as per Puppy of Kosh's post....
the /clr option means that you have enabled the Common Language Runtime, which GDK is, at least out of the box, incompatible with. You can also change that from project properties.
The only way that switch could have been set though, is if it was done manually, ie, you did it OR a non-GDK project type was started that included CLR support. Either way, you need to remove the references to the CLR as they will conflict with GDK, its unmanaged...
If it ain't broke.... DONT FIX IT !!!