@ceci03 What's struck me about your thread is that you are presumably upset about this and you're trying to understand what you can do to help your situation - otherwise you wouldn't have posted it on Mumsnet. However, you do come across as very entitled.
Here: I mean what about al the days I WAS at my desk even before 9? What about all the times I stayed an extra half hour to get a document finished ? I'm afraid that's rather normal. The start time is when you should be working from - if you get in extra early then that's bonus time for you to get your coffee in, do those random bits of admin a normal day never has time for, that sort of thing. The idea that if you're early you should be praised, that if you stay to finish your task you should be praised even more... I'm sorry, but that's normal (or at least your manager thinks it's normal) and you sound very put out. I suspect this attitude can be "felt" in the office.
Here: She goes at 4pm so never saw that. Maybe I should have been more pushy about pointing it out. She will be hearing things about you from colleagues, though. She'll get a sense of the work you're doing too. Don't track every second you're at the office - if you're early, you're early. If it really grinds you down that you can't "bank this time" then you're going to need to find another way to look at it. Take a book in? Most people won't get in at precisely the right time to clock-in (whether precisely or not) because of buses, trains, all the rest of it. It is your job to manage your time properly so that you are always on time, or early.
Here: One of the days she came to find me just after 9 I had gone down to IT as j couldn't log into my computer. Probably valid, yes, but it sounds like you have an excuse for everything. As your manager, I would be highly sceptical when everything has an excuse.
Please don't get me wrong, I don't think you're this conniving. But you really don't come across well. You haven't been in the company long enough, and, as others have rightly pointed out - you haven't "banked" up enough brownie points to be doing things like using up lunchbreak time. What happens in the first few months, of what is normally a probation period, is extended into the normal work. So I imagine your manager is thinking "if this is what she's like when she knows she has to make a good impression, and is on her best behaviour, what on god's green earth is she going to be like when she's settled in".
This is interesting: Even this evening there was a document I hadn't finished even tho she asked me for it before she went home I didn't stay late to finish it.. Do you mean here that your managed asked you to finish something by the end of the day, and you've not managed to get it done during normal working hours, and you didn't stay to finish it either? It sounds like there's a mismatch of expectations. I suggest that tomorrow you speak with her about why you weren't able to get it done during the day - nicely! - but be aware she may be thoroughly peeved that she can't trust you to "behave" when she's not there.
Your "lucky last boss" sounds like she was royally taken advantage of. Your new manager doesn't take any shit, and I'm afraid this learning curve will be very painful for you if you continue to resist her efforts to show you how most people are capable of behaving in a fast-paced office environment.
I'm sorry to not be more sympathetic. I was hoping to. I've been there with micro-managing bosses. This one, however, sounds like she's seen a bit of what you can be like and has drawn her own conclusion as to what you might be like when you're not micro-managed! She may be wrong, but the only way to prove that is to buckle down a bit and figure out how you're going to make this job work.