Latitude E7240 A10 bios update + bios settings change corrupt data drive

Hi, We have come across an issue where if we change bios settings using CCTK after an update (or attempted update) to A10 then the hard drive becomes corrupted and windows will not boot. We use MDT 2013 to script our O/S installs. The process includes attempting to install the latest bios update so when we roll-out new laptops or repair existing ones it will always have the latest bios installed. If the laptop has the same bios version as the update, it produces error 3 and the update doesn't go through as its the same version and we do not force the update. The laptop reboots in either case. Next stage is to use CCTK executables to set a bios password, turn on SMART, turn on the TPM module and then clear the bios password. The CCTK executables are built using compatibility mode. After the CCTK executables run and the laptop restarts, we then get the corrupted hard drive. If I turn off the bios update and just run the CCTK stage, the laptop hard drive is fine. This doesn't happen with any other laptop we use ( Latitude E6xxx series) or workstation (OptiPlex 7xx or 9xx). The log files from the bios update and the CCTK executables look fine and have no errors. Any ideas?