You are doing the right things to help your son feel good about himself and his abilities. Keep explaining that it's not his fault that he's behind, and that you and his teachers are going to do everything you can to make sure he catches up. Be sure to praise your son when he is successful and can do the things he is asked. Help him feel good about what he does know, and work with the teacher to support him as he moves forward.
Switching school mid-year can cause academic difficulty.
I have an eight-year-old son who switched schools at mid-year. I asked the system whether or not they thought he would have a problem adjusting to a new place during the year, and they told me he would have no problem. Now he is having problems trying to catch up with what he missed during the first half of the year. They are going to perform some tests on him to see if he is eligible for help. How do I help him maintain his self-esteem during this stressful time? He seems to think we are mad at him. I tell him that we're not mad and that we just need to help him catch up. Am I handling this the right way? Do you have any special tips I could use?
When the school told you there would be no problem, they were probably thinking about problems with social adjustment, and not that your son would be behind academically. If they are testing him, the school staff may suspect that there is a problem greater than simply being behind because he was at another school.