Further signalling problems caused delays to services between Havant in Hampshire and Chichester in West Sussex, between Shrewsbury and Wolverhampton and between Yeovil Junction and Salisbury in the West Country.
Another signalling problem, at Wandsworth Common in south-west London, led to delays to services through Balham station in south-east London, while illness to a passenger resulted in delays to services between Shenfield in Essex and London's Liverpool Street station.
No trains were able to run in and out of Moorgate station in London due to a lineside fire in north London. There were also delays in and out of another major London terminus - Waterloo - due to a signalling problem at Clapham Junction in south London.
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The RMT union has accused Southern of inventing figures which the company claims show record numbers of guards are going sick.
Thursday morning's weather for the west of the region
Thursday morning's weather for the east of the region