Looks like the new signalling system put in during the CTX rebuild (4 years ago) had a meltdown this morning, disrupting service so badly that CalTrain is offering free rides today and tomorrow (Friday) as an apology.
Customer ALERT: The computer problem which caused today’s train delays has been repaired. Train delays are expected to continue through the afternoon, as crews work to restore service. As a gesture of apology, all rides on Caltrain will be free until 1:30 a.m., Dec. 5. In addition, Caltrain tickets will be honored on VTA Routes 22 and 522 (which serve Caltrain stations) and on all SamTrans buses for the remainder of the day.
Update: I overstated this: "As a gesture of apology, all Caltrain rides were free from 1 p.m. to the end of the service day. We regret the delay and will continue to work to provide the service our customers expect."