My Human Resource mgr says that if the associates don't start clocking out for 1 hr for lunch, she will go in the computer where our time is managed and take out the lunch hour herself. Can she do this?

She can as long as you are actually taking a lunch. If you are not taking a lunch, she must pay you for the time you work. However, she can discipline you for not clocking in and out.

The main problem as she sees it is that the standard lunch is 1hr; some associates are only taking a 30 min lunch (without permission to do so) then going back to work after the 30min are over. This way they get in more time. The company wants everyone to take 1hr unless they have permission to do otherwise. So if I understand you correctly, if we are actually working after the meal break, she has to pay us for that time, regardless if she thinks we should have stayed an hour at lunch. Could you quote me the GA code for this? I would like to point her to this so she can revise her thinking so she doesn't get into trouble.
Thanks for your time!

You can read about it at: http://www.dol.gov/esa/regs/compliance/whd/whdfs22.htm