Sounds like he is having meltdowns. This is typical behavior for austistic kids. It is their frustration, anxiety and inabilty to communicate their needs. Sometimes just wrapping him in a blanket and applying deep pressure can help. It's nearly impossible to 'reach' them when they are having a meltdown. Watch for the triggers. Sometimes you can ward a meltdown off. If it is possible, and he is not harming himself or others, let him work though it. Walk away. If you can, teach him other ways to deal with his frustration. Breathing exercises, a punching bag, etc. are some ways to help.
Check out the autism boards. The parents there can give you some great ideas.
Your son's situation is so complex that a doctor really needs to look at the meds. Who is seeing him now? Is it a neuropsychologist or pediatric neurologist? If not, that's where I'd start. A ped isn't going to have the answers. If the doctor isn't helpful, find a new one who will actually listen to you.