Java HotSpot Virtual Machine

Here's my case.

(C++ Class) <-> (JNI/DLL) <-> Java Wrapper <-> Simple Java Application

With the above case, I have no problem with the java application.
Everything is working correctly. But..

(C++ Class) <-> (JNI/DLL) <-> Java Wrapper <-> Complex Java Application

The above behaves differently. There were method/function calls that does not return the desired result. Instead of an appropriate value, zero is always returned.

BTW the functions called were microsoft functions. eg.
RegQueryInfoKey, HrQueryAllRows.

Any ideas?