Hi James,
I have been in contact with various people in NI and we believe that most of the problem is due to the way which you are measuring the VI.
Attached is a revised project.
There is also an example which shows the way to time a VI - C:\Program Files (x86)\National Instruments\LabVIEW 2012\examples\general\structs.llb\Timing Template (data dep).vi
An additonal feature would be to change the compiler settings in Tools >> Options >> Environment >> Compiler. Setting this to 10 which should keep optimization at rarely limit.
This should avoid any major fluctuation in compile and the time which the VI takes to run.
Regards,
Nathan
Applications Engineer
National Instruments UK & Ireland