Certificate Install Security Warning Workaround?

I have some C# 4.0 code that attempts to install a CA (.der encoded) certificate into the "Trusted Root Certification Authorities" store for the current (My) user. My little console app runs silently against other stores, but for this store a GUI popup comes up "You are about to install a certificate from a certification authority... Windows cannot validate that the certificate is actually from..... Do you want to install this certificate?"

This messagebox is a problem because the idea is to automatically deploy the app with an MSI and silently get the right certs in the right place. Having a modal box will kill automated deployment.

How can this installation be done without a deployment-breaking messagebox?