I think there is a clause that gives the US free access to anyone they deem connected with the nuclear arsenal, weaponry, whatever, without the right of Pakistan to interfere on behalf of their protection or protection of national security.
I don't know if it was changed or not. But basically that means if they have reason to believe YOU have some connection with the nuclear facilties, they can pick you up and interrogate you on their own grounds, their own rules.
I can understand why a country would see that as stepping over sovereignty.
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Again this is more of a myth then part of the actual bill. Funny how most people are "analyzing" about the bill without knowing what is written in it !!!!!