I am guessing you want to keep your automation folder, but do not want the 30 second delay at startup with the boot option menu. This delay is added by sysprep when you deploy an image. DS 7.1 correctly creates the boot option for the automation folder with no delay initially, so before you capture the image everything looks good. Sysprep resets the timeout to 30 seconds if there are multiple boot entries during deployment, and as far as I can tell there is no way to prevent this. What we did as a workaround is to add RunSynchronousCommands in our answer file to export the boot entries to a file, then delete the automation entry:
<RunSynchronousCommand wcm:action="add">
<Order>18</Order>
<Description>Backup Boot Entries</Description>
<Path>cmd /c bcdedit /export c:\boot.export</Path>
</RunSynchronousCommand>
<RunSynchronousCommand wcm:action="add">
<Order>19</Order>
<Path>cmd /c bcdedit /delete {e217309d-dead-beef-a315-001372be0d01}</Path>
<Description>Delete Altiris Automation Boot Entry</Description>
</RunSynchronousCommand>
<RunSynchronousCommand wcm:action="add">
<Order>17</Order>
<Description>Reset Boot Menu Timeout</Description>
<Path>cmd /c bcdedit /timeout 1</Path>
</RunSynchronousCommand>
This means during deployment there is only one boot entry, so the timeout doesn't get reset Then after image deployment and reboot to production we restore the boot entries from the exported file with a run script task:
REM Restore boot menu with Altiris Automation entry
bcdedit /import c:\boot.export
del c:\boot.export
You could alternatively skip the answer file portion and just run "cmd /c bcdedit /timeout 1" as a runscript after deployment, but this means that your reboots during windows setup will pause at the boot entries for 30 seconds multiple times (since win7 setup reboots so often). We didn't like that so went the extra mile.