Hi Jeffrey,
Did you find a resolution to this? If not, I'd recommend reaching out to FileWave Support since you say it works when you run it locally but not when using FileWave. The only thing that comes to mind is if it requires User input during installation, but if it's a silent install it should work with FileWave too.
You can contact Support at help.filewave.com or help@filewave.com
Thank you,
Derek