Right now, in QV10 an extension that is running a .jar file will not work in QlikView Desktop, but WILL work when you put the same extension on a QVS and access the file via the AJAX client.
I'm not 100% sure, but my guess is that this is due to limitations in the embedded browser control that QlikView Desktop uses to render webview.
So if you want a .jar based extesnion for client server, all you should need to to do is build and test the extension against the QVS instead of QV Desktop and it should work.