M.T.
How long do you leave her in the crib before you go in to take her out? I notice that if I go into my daughters room as soon as I hear any signs of her being awake she tends to cry more and have a problem. I usually let her be in her crib for awhile after she wakes up before I take her out. It gives her more time to wake up without over stimulating her as soon as she wakes up. Also if she is still a little out of control after she wakes up I just let her go through her "thing" until she calms down and then I will start to give her attention. The only other thing that I can think of that it might be is she could be having nightmares of terrors and at that point you really need make sure she is in a safe place and let it go until it is over.