When I do a strip wash I put the baking soda in the machine as it fills, add the inserts (don't soak the outers!!) then pour the vinegar in, let the machine go for a minute or 2 too thoroughly mix everything up, then stop the machine and soak for the day/overnight. Then I let the machine finish out the cycle (with outers), then rinse again. If that doesn't work I do another hot wash with baking soda and put vinegar in the fab softener part.
And I always put the nappies through a rinse cycle before washing or striping, to get as much urine out as possible.