In separate figures just for the period 17 October, 1999, to 8 January, 2000, three companies - Great Eastern, Cardiff and Virgin West Coast - achieved improvements.
Passengers going between London and Glasgow Central on the east coast were being advised to take Virgin Trains' West Coast trains instead.
The transport secretary had earlier announced that Virgin Trains will run the West Coast Mainline for a further 23 months.
It follows a government decision to allow Virgin to continue operating the West Coast line, while new franchise bids are gathered.
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President John Clayton is concerned Virgin's franchise for the West Coast Main Line is only temporary and said the Department of Transport must not look for a "quick fix".
The mistakes came to light after bidder Virgin Trains, which had run the West Coast Mainline since 1997, launched a legal challenge against the decision.
The mistakes came to light after rival bidder Virgin Trains, which has run the West Coast Main Line since 1997, launched a legal challenge against the decision.
Virgin may be asked to maintain its west-coast service, at least for the time being.
Virgin Trains, which runs services on the West Coast mainline, told the BBC there was a "wider range of value fares than ever before" on their services.
The east coast was ten year old, ten year old, ten year old - sorry ten year old track, ten year old trains - and was really quite a modern railway network, and yet Chris Green and the team at Virgin Trains actually got the performance of the west coast ahead of GNER in the last six months running up to Hatfield.
Virgin will continue to run rail services along the West Coast mainline until November 2014.
Morgan, an investment bank, Virgin is part of a consortium that holds the West Coast and CrossCountry franchises.
The most popular rail company, according to the Which? survey, was Virgin Trains (67% satisfaction) which almost lost its West Coast main line franchise in October.
Virgin Trains, which was given the right to run the West Coast line for a further two years while the system is sorted out, is understood to be keen to bid for the new East Coast contract.
The West Coast mainline, he said, was continuing to improve and he was confident that Virgin could "build and sustain" the service.
Virgin boss Sir Richard Branson said his company would "try to continue to do a great job" on the West Coast Mainline now that it had been allowed to run the service for another 23 months.
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