To change whether SEP services start when the computer starts or when SEP starts do the following.
1. Open up the SEPM console -> Policies -> Antivirus and Antispyware -> The appropriate antivirus policy
2. Click on the File System Auto-Protect tab
3. Choose the advanced tab
4. For "Load Auto-Protect When: ", choose the button in front of "Symantec Endpoint Protection starts"
5. Restart the computer
Note: This only works (i think) when the computer is managed.
Go ahead and give this a shot. Obviously this is not ideal security wise. The longer you wait to have SEP start the more vulnerable you are during start up. However if this works it might help us determine exactly what the conflict is during start up that is causing the issue.
Cheers
Grant-
*edit* I forgot to mention that by default Auto-Protect starts when the computer starts and not when SEP starts.