Muni doesn't run this directly; it's contracted out to NextBus, a division of Cubic Information Systems since 2013. The NextBus web site says their vice president of engineering is Molsen Fahim.[1] But his LinkedIn profile says he left that job in March 2016 and moved to Cubic in another role.[2]
NextBus's interim general manager is Blair Brown, and his LinkedIn profile says he's been "interim" since 2015.[3] He was previously chief operating officer of Temple Beth El, a synagogue, and previously held some sales jobs, including being head of sales at NextBus in the past.
So there's the problem. Cubic bought a working system, the technical people left, and the sales types now in charge can't keep it going.
[1] http://nextbus.cubic.com/About/Management-Team [2] https://www.linkedin.com/in/mohsen-fahim-7035a34 [3] https://www.linkedin.com/in/brownblair