If the machines aren't making chips then they aren't making money, so that needs to be addressed. With you being the new guy making waves might not be the best idea. Going to your supervisor with the issues might be OK if you approach it carefully, but in addition to presenting the problem, presenting some solutions at the same time would be a good idea. Maybe you can come up with an easy way of becoming more efficient yourself to minimize the downtime. Obviously you can't set up two machines at the same time, but revisiting the workflow is sometimes helpful.
I'm going try to run two operations on two mills tomorrow, each operation has a cycle time of about 3 minutes, plus some deburr time. Not sure I can do it efficiently, but I am going to move one of the mills closer to the other to facilitate workflow and minimize steps. I'll let you know how that works out.