Let me understand your problem first , are you trying to boot the machine using network boot option [e.g F12 or bios setting] to boot to PXE and its not booting to PXE where as from the running Windows OS , if you send the task of 'boot to PXE' then it is working ; Similarly ,if you choose Automation while booting the machine [By selecting Automation Folder option by pressing down arrow key from the menu] and it is failing to boot to automation and you have to go to Windows OS and then send the task for this;
Is above understanding is correct ?
If the PXE server is configured properly and client machine set for network boot and if from the task it is working fine then i don't thing there should be a problem for booting manually ; similarly if automation folder is installed properly and it is working from Windows , then it should work properly manually.
Please confirm and provide more details.