If something is still holding on to the port, then a process isn't getting terminated like it should when you stop ArcGIS Server. After doing the NET STOP but before doing the NET START, try doing something like this in the batch file:
taskkill /IM ArcSOC.exe
TIMEOUT /T 5
taskkill /IM ArcSOC.exe /F /t
taskkill /IM ArcGIS.exe
TIMEOUT /T 5
taskkill /IM ArcGIS.exe /F /t
taskkill /IM ArcGISServer.exe
TIMEOUT /T 5
taskkill /IM ArcGISServer.exe /F /t
To schedule the stop/start, run the batch file via Task Scheduler but make sure it is set to run even while the user account for the task is not logged in.
Another way to troubleshoot this is to rule out anything else that might be using port 4000 (and the other ports used by AGS). To do this, stop ArcGIS Server and kill all its processes and then run netstat -a -o -n > c:\temp\port_use.txt from the command line. Look for any entries in the resulting port_use.txt file that seem to be using the ports in question. If something else is consuming that port, then there may be a conflict with AGS.
