Yep, the biggest issue is our lack of runs. Yes we aren't running through many teams but we're also a) not giving them much to bowl to and b) giving them enough to sit down and rest between innings.
The Test that sticks out in my mind is India, Napier, 2009 (?) We made 600 odd on an absolute road and although it was flat as hell, the sheer weight of our runs affected India's mindset and we made them follow on. We didn't win the Test but we gave them a damn good run because we created scoreboard pressure. And from memory our bowling line up was Martin, Franklin, O'Brien, Vettori and Patel. Hardly earth shattering on a featherbed against Sehwag, Tendulkar, Dravid, Laxman etc. But it worked because we posted the runs. Same as India in late 2010 - we got runs and put pressure on them. In the third Test we didn't, and suffered.