CHICAGO (CBS) — The chairman of the Regional Transportation Authority said Wednesday the problems with the Ventra fare card system amount to “systemic failure,” not just “a computer glitch.” And he ordered his chief auditor to determine how much it’s costing.

RTA Chairman John Gates said he’s heard a lot of explanations from the CTA and its vendor, Cubic Transportation Systems. He told auditor Michael Zumach that he wants a “rapid and independent” analysis.

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Gates’ top priority is to determine how much the breakdowns have cost — in terms of unanticipated roll-out costs, lost fares, keeping employees on board who were supposed to be laid off mid-December and other hidden costs.

CTA, for instance, estimated last week that it let 15,000 people ride free when 165 Ventra card readers malfunctioned at 60 of the CTA’s 145 ‘L’ stations. Gates wants to know how CTA came up with that figure and other figures on unanticipated free rides given because Ventra fare equipment was not working or was unacceptably slow.

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Both Mayor Rahm Emanuel and CTA President Forrest Claypool have said Cubic will not get a dime in payment until it meets performance targets, and will begin weekly performance updates later this week. Until then, CTA continues to sell magnetic-stripe fare cards and will continue indefinitely to honor its old Chicago Card and Chicago Card Plus. The magnetic-stripe card machines were supposed to be deactivated this week, but that has been put on indefinite hold.

In addition, the RTA board asked Zumach to determine if it is possible to recover some of the money paid to lawyers and public relations specialists by Metra during and following the ouster of former CEO Alex Clifford, and whether the agency can collect anything under an insurance policy it purchased shortly before the controversy heated up.

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Zumach said Clifford is looking for work. The longer he takes, the larger the payout to Clifford, which could reach $871,000. Zumach said the costs, when figuring a maximum payout plus other expenditures, would run well over $1 million.