I'm not very experienced with builds - this may be really easy! I have a simple application with a simple deployment project. I went to the directory where the release-compiled versions of the DLLs are, signed all of them (verisign), and then went to the deployment project, chose Build (not REbuild), and it recompiled all my assemblies and now they aren't signed any more. Can I keep the nice easy deployment project and still have signed assemblies, or do I have to create the MSI a different way? Thanks!
Try signing the assemblies as an intermediate step of your build.
One way to do this is to add a dummy project that has a build event that signs your assemblies. Make this project the last step before you create your MSI package.