The first thing I, and especially support, will want to clarify is that you're not using pre-release versions of both VSC and DOT. I'm hoping you meant 4.1P1 and not 4.1X1. If you're using X1, please upgrade! That is considered a Beta build and likely did have some things we've since fixed.
Also, I know there are TONS of things that have changed for the better between 8.1RC1 and the more current 8.1.2 release.
I cannot comment on the specifics of what you're asking about user permissions, and whether or not it is directly related to those older pre-release builds, but please get those guys upgraded ASAP!
David Kelly should be able to assist with the RBAC tool.