My youngest son suffers from separation anxiety from birth. I didn't know it until he was 2.

After I gave birth, my son went home but I remained in the hospital for 4 solid months. He was well cared for by my mother. When I finally got home, my baby would wake up every 30 minutes to an hour. Like most of us, I just endured it. He was always very clingy to me and he was on my hip until he went to kindergarten. When he was 2 years old, he got up and walked into my bedroom and said "I just wanted to see if you were still here". I was a stay at home mom, home 24 hours a day and 7 days aweek. If I went anywhere he came with me.

What I did was I held him, and stayed close to him. by the time he went to school, he was ready to be with other kids. But even to this day (he is 10 years old) he comes to sit with me, kisses me 100 times aday.

I think the best way to handle it is to continue to enforce his security level. Never say to him "if you don't hurry, I am going to leave you here". spend the extra time. You will be glad you did.