Nick,
After checking that a up to date agent was on the Pxe Rep I uninstalled the existing Pxe services and files rebooted and ran the Pxe deployment script and it did nothing but the scheduled task showed success but no files were deployed or services started.
I then ran just the OSDREP.msi and everything installed.
I also found why the BCD file was not being copied even from running the OSDREP.msi. Whoever made the script had 2 REMCOPY 6 commands, the second was for the BCD file, I changed all the numbers and now it copys the bcd file.