The problem you are experiencing is a normal behavior. This is due to the fact that the TSAPI server from Avaya does not push the events over the ASAI link. This means that if you place a call or answer a call directly with you phone or call master, Genesys will not be aware.
Same thing with the state of the Agent, that is why there is an option in TServer for Definity called ‘queryagentworkmode’.
Conclusion: The problem doesn’t come from Genesys but from the way that the Avaya TSAPI server works.