Greater Anglia services in and out of London's Liverpool Street station were affected by a signal problem, with one of the London to Shenfield in Essex trains having to be cancelled.
A broken-down freight train has caused disruption between Clapham Junction and Kensington Olympia in London.
The London Midland staff problem mean buses had to replace trains between Bedford and Bletchley and also between Watford Junction and St Albans Abbey.
Last week the Government announced that London Midland season ticket holders would be getting five days' free travel in compensation for the continuous problems they had endured.
A white Christmas dream turned into a wet Christmas nightmare for millions of travellers today. as continued heavy rain played havoc with road and rail journeys.
This has included disruption on First Great Western between London Paddington and Bristol Temple Meads, and between London Paddington and Swansea due to flooding between Swindon and Bristol Parkway.
The mainline remains closed. All services are being diverted via Bath, with journey times extended by up to 45 minutes. Buses will shuttle passengers from Patchway to Bristol Parkway for connecting services.
Latest on the rail failures and floods which are hampering people's Christmas getaway
- A signalling problem in west London meant the Heathrow Express was unable to run
- It also caused delays and cancellations to Paddington services, with those travelling to Cardiff, Reading, Bristol and Bedwyn in Wiltshire among those affected
- Train services near Gatwick airport, in West Sussex, were also affected by a major signalling problem caused by an overnight fire at Preston Park near Brighton
- Motorists had to contend with floods in Reading and Henley-on-Thames in Oxfordshire causing long queues on non-flooded roads
- By early afternoon congested spots included the M25 in Essex
- Travellers trying to reach Gatwick by road were held up by a sliproad jam on the M23 close to the Sussex airport.
- Major congestion built up on the M2 in Kent and the M4 in Gloucestershire
Newcastle Airport says it will handle 80,000 passengers over the Christmas period and they will travel on more than 800 flights across 10 days.
And today passengers at the airport said they were running smoothly.
Graeme Mason, airport director, said the flight traffic was as much people arriving home and there is a "real community feel" at the airport with people holding "welcome home" signs at arrival gates,