We had this with DD from nursery up to year 2. So from ages 3-6.
I do know that the 'gatekeeper' (an older 'retirement age' woman whom I'd known for years as such a lovely person) was incredibly strict behind closed doors. The children were terrified of her. She was old school and very polite to parents. But if you volunteered at the school and saw her in action, she could be a dragon. Some kids were fine, water off a duck's back. For example, DC1 didn't like her at all but the 'gatekeeper' had no effect on his happiness at school.
DC2, our DD who cried every day, is sensitive and feels things more. Her emotions rule her, which is wonderful but this also means that the more painful stuff gets to her in ways they might not get to other kids.
So this 'gatekeeper' was just such a dark cloud for our DD. DD dreaded going to school to the point where she couldn't even articulate what it was that made her so unhappy. She was so sad, so tearful every day. We couldn't see the forest for the trees.
It was incredibly, incredibly stressful, sad, and tedious.
We moved schools eventually because we were leaving the faith school system and wanted to put our DD in another non-faith primary attached to DC1's secondary school for easier transition later.
That was our reason. There wasn't a lot of love lost because the crying every day at the school gates was so trying.Still, we didn't expect it to improve at the new school. We expected it to get worse.
We were wrong.
DD moved in the middle of year 2 and never looked back! The change was unbelievable. She never cried again. I can't help but feel that she was deeply unhappy at her first primary school- a lovely school for so many reasons- just not lovely for DD.
I wonder how happy your DC is at school? Kids are quite good at 'coping' and wearing a mask, leaving others unaware of their unhappiness in the very environment that brings them distress. Although it may be too late to move, I don't know what your thoughts are on that, there maybe something surprsingly very simple that is upsetting your DS, something he may no longer even be able to articulate because the distress has gotten so on top of him, so habitual, that the cycle can't be broken. A change might break the cycle/the habit and remove whatever it is that is causing his distress (a grumpy member of staff who gets to him, a kid in another year who gets to him). We expect our kids to buck up, cope, crack on. But for some kids this is more difficult. Do you have any idea as to what might be causing his tears/anxiety?