Can you check to make sure that you have followed the directions from the The Java Developer's Guide to JTwain v9.
6.3 Software Packaging and Distribution
There are two files about JTwain you need to distribute along with your own binary code. One is JTwain.jar, which is like any other java library, you can just copy it and put it in the class path. The other one is AspriseJTwain.dll, the native library. There are many ways to 'install' this dll file, you can: Add the folder containing the native library to the system path, or Copy the native library to jre/bin directory – 'install' the library to the JVM, or Copy the native library to a specific location, e.g. C:\AspriseJTwain.dll, before calling SourceManage.instance(), call: SourceManage.setLibraryPath(“ C:\AspriseJTwain.dll ”);