If I copy a masterpage and make changes to it (like changing the flow title in a text box or loading a different picture) the changes effect the master page I copied from as well…
That is as expected. Copy and pasted fields/frames are normally linked.
If you want a new field/frame, you have to create it fresh. I have found it very useful to jot down the Properties of the frame I am reproducing so that I can match the settings.
Normally that’s no big deal, but if I copy the text it looses its formatting. Any idea about this?
Yes, that’s the behavior at present. Many of us are looking forward to improvements in this area, but for the time being, you have to redo the formatting.