Not sure but try this one. Run regedit go to "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon" at the right pane add a string value "ParseAutoexec" (no quotes) and give value 1 to the string. Hope this help...
on the flipside, autorun is a function of any cd/dvd drive that executes when you insert the cd and the cd contains properly formatted file named autorun.inf
if you want the batch files to execute on windows startup, id place them in either A- windows start menu startup folder, which loads after windows logon or B- windows registry Run key Run and RunOnce Registry Keys
Under Local Computer Policy > Computer Configuration > Windows Settings >Scripts
There you can set start up and shut down scripts. Dont know if that helps?