That's pretty much my experience too. A good paper will use lots of citations, and hence have lots of flags from these services (eg turnitin), but this doesn't

That's pretty much my experience too. A good paper will use lots of citations, and hence have lots of flags from these services (eg turnitin), but this doesn't mean plagiarism - it means the student's doing the right thing: gathering supporting (or negating) evidence and quoting it for the purposes of argumentation.