Issues at Slough in Berkshire since Tuesday have caused two-hour delays.
It comes after Network Rail replaced old signalling equipment at Slough over Easter, and promised no rail chaos afterwards.
Network Rail spokesman Julian Burnell said: "We are really, really sorry that we've had all these problems."
Network Rail installed "new state-of-the-art technology" at Slough during the Easter break as part of a major re-signalling project.
It had promised no delays like those experienced by passengers in London over Christmas after engineering work overran.
But passengers travelling on the line from Banbury in Oxfordshire through Reading and towards London Paddington said a one-hour commute took up to three hours.
Commuter Bill Gibbons from Reading said this week had been a "pantomime".
Mr Burnell said: "Can we just forget about this week?  It has been an absolute disaster zone on some of the signals we've got.
"All I can say is that we are really, really sorry that we've had all these problems.
"It's not the kind of service we want to provide, it's not what we get out of bed in the morning to do.
"[But] it does underline how old and how rubbish some of these signals are.
"We did replace a whole lot of them, but unfortunately we didn't replace everything."
First Great Western spokesman Dan Paynes said it had been an "abysmal week" for their passengers.
He added those affected could apply for ticket refunds via the First Great Western website.
Network Rail has apologised for creating a "disaster zone" after three days of signal failures on the Banbury to Paddington train line.