I may be missing something but this has been bugging me since the begining of the season...

Why was Noah sitting in a cell in level 5 in "The Second Coming"? ... As far as i was aware Noah was released at the end of the last season so he could work (under duress) for the company again... Was there something I missed or was supposed to get but didn't? Any help on this would be greatly appreciated

I believe you are right he was working for the company in a sense, he just wasn't active as an agent yet. If that is not the case then he lied to his family to keep them from knowing what was really happening to him. He needed to be there in order to "contain" him, or just apart of his punishment. The key difference between Pinehurst and Primatech is that Primatech doesn't kill people they just contain, Pinehurst is darker more willing to kill. So rather than kill HRG they just contain him, its more "humane."

No, don't worry, it's not an idiotic question at all, I was wondering the same thing myself, but I think I know

HRG is only kept on Level 5 during the first two episodes, while Bob Bishop is director. This is because although Noah is a company agent, he is also incredibly dangerous and hates Bob loads, and given half a chance, he would kill Bob and return to his family. However, when Angela is director, she knows that HRG won't kill her because his top priority is capturing the escaped villains, so he's allowed to stay wherever he wants (presumably hotel rooms and stuff). Noah isn't a threat to Angela anyway, as he doesn't hate her and she's really allowing him to whatever he wants