If a company could weep, GlaxoSmithKline would surely be weeping now. It is difficult to open a newspaper without reading of the tribulations of the UK's largest pharmaceutical company.

Ever since it took the ill-fated decision to launch a legal challenge against the South African government's efforts to obtain cheap Aids drugs for its stricken people, Glaxo has been cast as the unacceptable face of the capitalist drugs industry.

The row over chief executive Jean Paul Garnier's $18m pay package put the company where it did not want to be - back on the front pages - in 2002. The same year it became embroiled in a row over the safety of the antidepressant Seroxat- its biggest selling drug - which still rumbles on. Last week, Eliot Spitzer, the New York Attorney General, warned the company that he would be watching it "with a hawk's eye" after he was angered by the "arrogant" way in which it had brushed off his lawsuit relating to Seroxat, known as Paxil in the US.

Spitzer had sued the firm over its failure to disclose research suggesting problems with the drug in children. GSK agreed to pay $2.5m (£1.37m) in damages to settle the case, and promised to publish all research in the future, but denied any wrongdoing.

Analysts said the compensation figure was a victory for GSK given the hundreds of millions that the company could have lost had the case gone to court. Spitzer complained that the company had shown too little contrition and had treated his lawsuit as little more than another legal annoyance.

I cannot say whether Spitzer's suspicions of the company's motives are justified, but I had a curiously unsatisfactory encounter of my own with a couple of its senior executives earlier in the summer.

Out of the blue I received a call from the company's head of press, Neil McCrae, inviting me to a private breakfast meeting with the medical director, Alastair Benbow, to discuss developments on Seroxat. The UK Medicines and Healthcare Products Regulatory Agency is conducting a review of the safety of antidepressants, including Seroxat, which is due for publication this autumn, so I was keen to see what they had to say.

Naturally I wondered why they had picked on me. Was it because, despite the current scare about antidepressants increasing the risk of suicide in some people, I have always defended the drugs on the grounds that they have saved millions of people from the misery of depression, which is a terrible, sometimes fatal, illness?

Dr Benbow seemed an honest and sincere man and the meeting, though less than an hour long, went well. I learnt that, although the MHRA review was still ongoing, Seroxat had already been cleared for continued use in adults by the European Medicines Evaluation Agency (EMEA), which regulates medicines in Europe, including the UK.

This gave me a story. Seroxat was the antidepressant at the centre of the scare and it had apparently been cleared even before the MHRA had completed its review. But when I checked with the EMEA, a different picture emerged. Seroxat had indeed been cleared, but with a crucial additional warning that extra caution should be taken in young adults, aged 18 to 30, who should be monitored in the early weeks of treatment.

A positive story - Seroxat cleared - thus became a negative one - new warning over Seroxat. When I contacted GSK to gently protest and inquire why they had omitted to mention the new warning, Dr Benbow responded that he had not had time at our meeting to apprise me of all the details of the EMEA review. He seemed, as I say, a decent man and I am loath to believe that he and McCrae set out to deceive me.

But it makes one wonder, pace Spitzer's protest last week, whether the huge sums of money at stake in the pharmaceutical industry may distort the judgement of otherwise decent men. It is all too easy, as we know from other contexts, for committed people to come to believe their own propaganda.

In 2002, more than two million prescriptions for Paxil/Seroxat were written for American children and adolescents alone, worth $55m in sales.

Spitzer's lawsuit sought to close the loophole that allows drug companies to use selective trial data to back their products. The multi-billion-pound pharmaceutical industry has become adept at manipulating results and selectively withholding data, thus potentially exposing patients to harm. The episode re-emphasises the need for more drug trials to be run by independent research organisations with state or charitable funding. The task of ensuring safety is too important to be left to the drug companies.