What's the reason for the guvnor update? Do you need 5.3.0 for any specific reasons?
With jBPM installer 5.1 I believe you cannot use Guvnor 5.3.0. jBPM console will not be able to parse your pkg's from Guvnor. You should see exceptions in your logs when console lists the processes for the first time.
Either use the Guvnor version that ships by default in installer, or you can try Guvnor 5.2.0.Final and let us know if you still run into issues.