I couldn't wait any longer for a resolution or explanation. I went ahead and ran Install repair. I bypassed the installers desire to reinstall Visual Studio 2010.
Preflight is again functioning.
I have escalated this to our regional helpdesk also.
I have noticed the error has appeared on another machine overnight. I have a feeling it could be related to a license issue within the software.
It is affecting all preflight presets and the optimise node. the preflights were the standard "fix ups".
I ran the systemCheck.exe and the only warning it comes back to is and unknown edition of SQL Server (evaluation). See attached. Is this enough to prevent preflight from running? Is there a dependency on this?