MBTA officials say they believe they have solved the problem that bedeviled thousands of commuter rail riders this morning who tried to get on the subway once they arrived in Boston but found their newly issued CharlieTicket monthly passes rejected by automated fare gates.

“We just had a successful test with the fix,” MBTA spokesman Joe Pesaturo said. “The fix is being distributed to all the fare gates throughout the system so we’re optimistic that all of the people who hold passes from the corporate pass program will be able to access the subway on their way home.”

The issue was indirectly related to the fare increases that took effect Sunday. While updating software for all vending machines, fare boxes, and fare gates, a glitch occurred in the software that recognizes monthly commuter rail passes sold through the corporate pass program when used to transfer at subway fare gates. That affected as many as 25,000 riders, causing backups and confusion at subway stations when those riders tried to use their passes, officials said.