I am going through this with my 5 yr old Ds at the moment too.
He had a short time in nursery where hecried going in, but it stopped after about 6 weeks.
He started Reception in Sep and went in fine, loved it etc, then he got the flu bug going about at the end of Nov. After that we had so much trouble with him being upset that his teachers thought it best he stayed at home till after Xmas. This wasn't something I was happy about, but although I tried to get him into school , they said he was so upset they thought it best he stayed home.
Now come January, he thinks if he says he's poorly or he gets upset, he will not have to go in. So, every morning I get crying from about 8 o'clock till he goes in at 9.
At the beginning of term I explained to the teachers, and they are now being very good and just come to the door, and take him in.They say he settles very quickly, he's having no problems and gets on well with every one. He comes out every afternoon, full of beans and excitedly telling me about how wonderful his day has been, every evening I think he'll be better tomorrow, yet in the morning we are back to tears again.
I think it's just seperation anxiety, I just hope it stops soon.