It's kind of hard to diagnose if we have no idea what you're actually doing. Got some code?
EDIT: I would wager that filtering in general is incompatible with MSAA surfaces, though. I can't really think of a good way to incorporate the extra subsample data in that operation and I suspect it's just blanket not supported for the same reason. If you aren't ResolveSubresource()ing right now, try that first (again, code!)