My son just started Reception a couple of weeks ago. He was 4 in the summer, but I decided he should stay in the school until 3 o'clock, because I was afraid that other children get picked him or something because he can leave earlier than them. Last year we had the same situation as you, he was in the nursery full time for the last month to get used to the long days.
The first week was ok for him, then I think he realized that he needs to go to this school for a long time not just for a week or something and he started to cry in the morning from the second week. After the first crying (because it was unusual for him, he never cried, except the first week in the nursery, when he was 2) I spoke to his teacher (she is very lovely) and we discussed the situation. I thought she will think silly women this is the second week what did you expect, but not, she was really helpful. We decided that one more time in the morning I go to the classroom with him and explain what the routine is (e.g.: where to put coats, bags drinking bottles) and explain that from next day he needs to do it alone, because he is a big boy. The next day I gave him kisses and let him go alone, the teacher was very nice, she was waiting for him by the door and helped him in the classroom. Since then we do not have any problem with the morning drop off. He is very proud of himself that he can go to the classroom alone. Now the teacher and I decided that from next week we say goodbye by the gate so he will have his own walk through the field to the classroom.
Teachers can help you a lot. I think it is very unusual that they do not even have eye contact with the child. Our teachers have time to speak with each child in the morning (probably because they ignore the parents in the morning and focus only the children). Children need this contact to feel comfortable and secure. Probably you should speak to the teacher to say Good morning to your daughter (even raise her hands if that is how she did in the nursery) and help her in the classroom. I think you should let her stay in the school until 3, because she gets used to it in the nursery and because at lunchtime they are having fun and the children socializing together. She won't feel so alone if she does all of these things with the other kids in the afternoon. Probably if your child?s class has a teacher assistant she can spend more time with her in the morning (saying Good morning, perhaps play a little game, or read a book) so she can forget you, the stress, the crying etc...
And also you can have a big long chat with your daughter about the school or even her sister can ask her what the problem is and talk three of you what is good in the school and what is bad. It is ok to have thinks what they do not like in the school, we have things that we do not like in our life but we need to get on with it. Every time I pick up my son I ask him what was the best thing in the school that day and what he did not like that much. Talking through bad things help children realize that the big bad things might not as big or as bad they thought.
Oh and one more very important things. I read this in here in another thread and I tried and it works. Children miss parents in the school a lot. Sometimes they cry because they would like us to be there. So every morning I and my husband give a magic kiss for my son to his hand and I tell him this is a magic kiss from mummy and daddy what you cannot wash out, but when you feel sad, alone or if you just miss us, you can look at this kiss you can feel this kiss, and you know we love you and think about you as much as you love us and we always with you in your hearth.
But definitely you have something to worry, because it is not good if she is upset for the whole day in the school.
Sorry for the long story, but I hope everything will improve very shortly.