The new managers of VU2 media, which went into administration in the summer, say that the 250 pupils who use the service each week have not been affected.
Officials from the Department for Education and Skills met members of VU2 last year because the Government is interested in using online classrooms to provide pupils with a broader range of subjects.
But the Hertfordshire company has suffered a series of major setbacks since its launch two years ago. Police were called in to examine one of the company's computers last year after staff raised concerns about "unsuitable material" prepared by one of the teachers.
VU2 Media's new managers said the teacher was dismissed immediately for improper conduct, the material was not transmitted, and no charges were brought.
The company's problems continued last autumn when the National Endowment for Science, Technology and the Arts halted grants to VU2 midway through a Pounds 210,000 project.
The trust could not say why it had frozen the payments but a spokeswoman said it had needed to put the company "under close review".
This summer VU2 went into administration, leaving nearly 100 companies and more than a dozen teachers and programmers unpaid for their services. At least four former staff are now taking legal action or bringing claims before industrial tribunals.
Graham Lawler, VU2's former head of maths, was owed more than pound;10,000. He said he was furious because VU2's "online classroom" had begun to show some success and that a growing proportion of the excluded pupils he taught had been reaching GCSE level.
"There were many times when we'd be staying up to midnight and beyond working on it," he said. Other staff lost up to pound;25,000.
VU2 Media's assets were bought by a different firm, VU2 Learn, which continues to operate the service under its original name.
Rick Belfield, its new managing director, said the new company had managed to ensure that pupils and local authorities had received a consistent service after the summer holidays.
"The pupils have been our first priority", he said.
Mr Belfield confirmed that staff in England and a small group of programmers in India would not be paid for work they did before the company went into administration. But he said that the Indian programmers appeared willing to "let bygones be bygones".