Auto in and manual In for Avaya G3

We have just recently installed Genesys 6.5. When we register an extension DN in Genesys it automatically begins to work in a Manual In mode even though the extension on the PBX is configured with as AutoIn. My assocaited is not registered with my sofphone application. Has anyone experienced this? I would like the phone to operate in AutoIn mode when the assocaited is not registered and operate as Manual In when they are registered with our softphone application.

Thanks

What desktop application are you using to log in?