Here is the original sentence:
In 2001, with the passage of the No Child Left Behind Act, that assumption was, as they say, no longer operative. By that time, more than twice as much money was being spent on each student, after accounting for inflation, as had been spent when NCLB's direct ancestor, the Elementary and Secondary Act of 1965, had been enacted and, though some progress had been made on student achievement, it was hardly commensurate with the size of the additional investment.
The simplified version of the part of the quotation I have question on is:
More than twice as much money was being spent on each student as had been spent when the ES Act had been enacted.
Instead of using "had been", I would say:
By the time the NCLB Act was passed, more than twice as much money was being spent on each student as was being spent by the time the ES Act had been enacted.
What confuses me is that "had been" is used to denote an event that happened, up to the point when the "was being" event happened. But what I think they are trying to say is that
by the time the ES Act of 1965 was passed, the money spent on each student is only half the money spent per student by the time the NCLB Act was passed.