Hello Hmann,
I'm not sure what's the behavior you talk about as you haven't provided an example, but I think this vi might help.
What you may need to do to avoid that behavior is to assign to each plot one Y Scale (you need to use the Plot legend to do this). I've done so in this example, and the Autoscale wasn't affected. Please let me know if this doesn't solve it and how to reproduce it step by step.
Regards,
Jorge M.