So basically (which I should have picked up on), it is the non direct costs that are higher…kind of like with charities how much of the money you give goes toward fundraising and administration, rather than the real work of the charity (where the analogy is the researchers, equipment, etc, are the ‘real work’.). I suspect the rest is what the school bills to the researchers, kind of like in a company they bill services like IT to various departments, gets charged against their budget. I wouldn’t be surprised if schools bill a percent of administrative costs (like admins in the chemistry department for a chemist doing research), the cost of paper clips and stamps the department uses, the dean in charge of faculty, the internal mail flow, etc.