The problem was first noted when Caltrain began service early this morning, spokeswoman Jayme Ackemann said.
Some trains were initially delayed by more than an hour, she said. As of 8:30 a.m., the delays were averaging 15 to 45 minutes.
"It's the computer software that controls the signaling system that's the problem," Ackemann said.
She said Caltrain has switched to its backup software, and hopes to have trains running on time again by the evening commute.