As of HF 3 then automation folder was introduced and then at hf4 automation partition removed as an option. If you haven't uninstalled your automation partitions on your systems they likely will continue to be used and will need to be uninstalled before the pxe or automation folders work properly.
In the boot disk creator you can right click on any of your configurations and you will have the option of a "Create Partition Uninstaller" this can then be used to clean up the autoation partitions if they are in place.
It may be that if you are now on HF4 you would need to create a new HF4 configureation in the boot disk creator and then will have the needed HF4 options including the right click install option.
Hope that helps.