Hi Gary,
I hope you are doing well today! What version of LabVIEW FPGA are you using? When you say you are doing 'alternate executions', what exactly do you mean? Do you run your host VI, stop it and then run it again? Have you tried just using Close instead of resetting the FPGA VI? Also, what are you using the reference for? What are you invoking? It would, also, be better if you post a screenshot of your VI.