Is there an Ex ability a protean could copy that would replicate the effects of the "Stop" scene?
It looks to be either Command (halt) or Fear (pass check causing shaken).
I can buy into the idea of the protean controlling its shape because that is an inherent ability of the creature itself.
I can also buy into the idea of the protean not controlling the abilities it is granted from copying the shapes of others because they are not inherent to the protean... they are something it is getting from another creature type instead.
Basically, it knows and understands what it can do, but it doesn't really understand what it is gaining from other creatures.