A fault with the signalling system between Uphall and Edinburgh Park affected services going into the capital, with a number of services on routes cancelled or altered.
The Bathgate route remains effectively closed as engineers battle the problem.
Train services between Glasgow Queen Street and Edinburgh via Falkirk Grahamston and Cumbernauld are still subject to cancellation, delay, or revision.
A separate fault at the Cowlairs Junction near Glasgow Queen Street compounded the misery of those trying to use the busy main route between Scotland’s two biggest cities.
That fault was dealt with by Network Rail engineers, but is still affecting services, dozens of which have already been cancelled due to the signalling issue.
Scotrail say they expect the disruption, which will have affected thousands of travellers on a busy bank holiday weekend when much of the country was enjoying warm weather, to last until around 7pm this evening.
Passengers took to social media to express their disbelief that the junction had been affected by a fault.
One wrote: “This absolutely boils me. How many times is there going to be an issue at this junction. It’s regular and beyond laughable.”
Another added: “Come on! How many times at the same place? Fix the problem! No more sticking plasters!”