The thing that makes the Greater Sanctuary bug a killer is that all the negative consequences of being in Greater Sanctuary still apply. (GS is far from an "I win" spell.)
Most importantly, you can't cast spells until the effect is gone. This includes using dusts.
Probably what happened is that you tried to use your second dust and it "fizzled" because of the still active GS effect.
What you need to do is to disable the effect. One way is to go into combat for a round. Or, if you prefer not to be killed, get a Rune of Sanctuary return and use it while running. Then use your second dust, and pray.