I have a overture connected to a ML/MCL convertor and using the mastelink cable only the amp does not switch on/off. Using the powelink the amp does switch on off correctly. Any idea on how to fix this?

I think this is by design: When connected by ML the Overture thinks that the ML/MCL is powering speakers in another room, whereas something connected by PL will usually be in the same room.

Does the ML/MCL go into stand-by after a long press on the remote's off button?

no with the pl its all instant.

I thought this is why you cant control the ML/MCL volume with the ir sensor.