You have to run simultanous 4 axis to get the stock model functionality. It doesn't take notice of the stock when running indexed, except for the area that's processed at the moment.
What you could do is either changing the post processor to always raise Z to a safe level when transporting, or you can simply select the transport paths and move them to a safe height in Rhino before you post process.
If you want to go for the first option you can send an e-mail to MadCam and tell them what post processor you're using and what you need and you'll get help with it.
Hope it helps!