The unions immediately objected to non-union labour being used to take the place of guards and other staff. But SWT retorted that it would carry on replacing striking workers until industrial action was "irrelevant".
The Rail, Maritime and Transport Union, whose members will walk out again today, said some managers were receiving only two days' training as guards instead of the usual eight weeks.
Aslef, the drivers' union, which is not involved in the strikes, wrote to the railway inspectorate last night accusing the safety body of showing "bias" to the train companies.
Mick Rix, Aslef's general secretary, said: "Whenever there is a dispute in the industry, the inspectorate seems more than willing to turn a blind eye to the poor standard of personnel used to beat a dispute."
But SWT insisted that its training of managers had been "safety-validated" and that it had consulted the inspectorate on its plans.
A spokesman for the inspectorate confirmed that it was satisfied that the managers had received proper training, but that it would carry out spot checks.
Rail disruption has taken place - or is being threatened - at seven companies, including at London Underground, and across a wide stretch of Britain from Scotland to the south coast.
The moderate white-collar travel and transport union, TSSA, joined the industry's mounting troubles by announcing a ballot of its station and ticket office staff at Arriva Trains Northern.
The first strikes are likely to take place in the last week of February. The dispute is over pay and conditions.
Steve Coe, TSSA's negotiations officer, said: "It is regrettable that we are having to resort to strike action, but the union has been involved in discussions for a month without reaching agreement.
"Staff are fed up at being at the bottom of the pile when it comes to pay."
SWT was able to run 600 out of its usual 1,700 trains across the south-west London suburbs and down to Southampton and Bournemouth.
It laid on more than 100 buses and coaches to replace cancelled services.
Some 35,000 commuters arrived at or left Waterloo station during the peak hours, but thousands still suffered long delays or overcrowding. The company achieved a far better success rate than on the first strike day earlier this month when it ran fewer than 200 services.
Andrew Haines, SWT's managing director, said: "We are determined that never again should the RMT hold our passengers to ransom.
"We cannot sit idly by while the RMT pursues its political agenda."
He went on: "We must take action to give our passengers the best possible service and our managers have proved themselves more than willing to go that extra mile."
Vernon Hince, the RMT's acting general secretary, accused the company of "deceiving" the public during the dispute. He said it would take years to replace guards, station staff, supervisors and other workers.
He said some managers used to replace strikers had never been guards while others had only been in the industry a short while.
RMT members who gathered outside Waterloo station yesterday for a rally attended by less than 50 demonstrators claimed that the public was on their side.
Alex Gordon, who sits on the RMT executive, said: "This is a clear attempt by a privatised rail firm to smash a trade union in a central public service.
"This is going to happen in the health service, the benefits agency and the fire brigade."
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