In Watford alone, a thousand 10-year-olds - around a third of the total - had no places after the first admissions round.
Two rounds later, there were still more than 500, although most have since been found places, according to the county council.
It says there are enough secondary places to meet demand. But in south-west Hertfordshire, where 10 of the 13 schools are grant-maintained, parents have had to make separate applications meeting different admissions criteria and deadlines.
Parents holding several offers of places have jammed up the system for other children who are desperate for a place anywhere.
The education authority had tried to broker a voluntary agreement with its GM schools on making the system more manageable in time for the 1999 intake, but eventually had to call in Mr Blunkett.
His scheme allows all Hertfordshire schools to retain their current admissions policies, but makes the county council a clearing house - ensuring parents are not holding multiple offers while some children have none.
Council spokeswoman Kate Robertson said: "We are pleased - it is going to guarantee every child an offer of a school place. It has been an anxious time for many children and their families, especially when they have been waiting right up to the end of the summer holidays to hear whether they have got places."