Secondaries are a source of revenue for medical schools. While many schools screen, it's far more cost-effective not to. Screening takes personnel away from applications, and even if the process is done in an automated fashion, it still costs the school money. Assuming that each secondary application costs $100 and a school gets 10,000 applicants:
$100 * 10,000 = $1,000,000 assuming all applicants fill out a secondary.
Now, if half of those students are screened out:
$100 *5,000 = $500,000
Thus, by screening, the school has lost $500,000 of income which could be used to hire more admissions staff.
So, as you might imagine, it's much better for the schools, though not you, to send out as many secondaries as possible. Even if you don't end up finishing AMCAS and getting verified, you might end up turning in a non-refundable secondary, meaning that you will have essentially given the school a donation since it has no obligation to review unverified applications.