Muni passengers frustrated by the rocky transition to the new Clipper card will finally get a bit of good news regarding the one-stop media fare.

Starting tomorrow, the Municipal Transportation Agency (MTA), which operates Muni, will waive its 25-cent surcharge on its new 90-day Clipper card ticket. The ticket, a reusable card, allowed for single-ride travel on Muni’s system. However, instead of costing $2—the price for a normal single-ride ticket—passengers were paying $2.25, due to a 25-cent purchasing surcharge.

MTA officials said the surcharge was a cost-recovery fee designed to cover the expense of inventory control, production, and administratives fees. Customers, however, saw it as a fare increase.

By suspending the 25-cent surcharge, the MTA will change the second major component of its new Clipper card technology. Along with the card problems, the MTA is currently fixing its new $30 million fare gates so that they don’t open with a wave of the hand.

wreisman@sfexaminer.com