CHICAGO (CBS) — Two months of quarrels over a who should get a $180 million dollar slice of the Chicago area’s transit budget ended Wednesday much the way it began, and not everyone was happy with the 14-to-1 vote by the Regional Transportation Authority board.

At issue was the pot of money the RTA considers its “discretionary fund,” but which has been given historically, for the most part, to the CTA.

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The feuding has put budgeting for 2014 weeks behind schedule, and prompted a warning from RTA Chairman John Gates.

“We are getting to the point where, if we don’t reach a consensus…we will kick off a series of events that will cause a significant disruption in transit early next year,” he said.

The result was an impromptu 40-minute closed-door negotiation. But the agreement kept intact the historic division of the supposedly discretionary funds: 98 percent to the CTA, 2 percent to Pace, while essentially forgiving a $56 million loan to the CTA that CTA has characterized as a grant and offering Metra $2 million for capital projects. CTA will continue to get 98 percent of the discretionary funding through at least 2016.

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DuPage County Commissioner Tonia Khouri ordered the county’s representative on the RTA board to vote no, and asked after the meeting where the compromise was.

“We don’t believe that’s fair allocation of the discretionary funding,” Khouri said. “The CTA getting 98 percent? Pace getting two percent? Metra getting zero? A formula needs to be made. What the specific formula is, we’re discussing.”

A consultant, meanwhile, presented a report that called for an overhaul of the RTA. Delcan Corp. offered eight different scenarios. Its preferred formula was a combination of distributing some financing based on geography, some on how well agencies perform and some based on a competition for grants.

The RTA, CTA, Pace and Metra are financed largely by farebox revenue and sales taxes that are allocated by formula, although the RTA decides which agencies get the discretionary money and in what amounts.

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It’s the second consecutive year there have been disagreements over the discretionary funding, which represent sales tax revenues above those projected for Chicago-area mass transit.