The scientist who proved that smoking tobacco causes lung cancer was subsequently paid by Monsanto and other chemical companies for 20 years, even being paid by them to investigate a specific chemical; he concluded that vinyl chloride did not cause cancer, a conclusion that the World Health Organization subsequently rejected. Was his conclusion influenced by his conflict of interest?

It is true that, when that was published, there was no rule about stating conflicts of interest. The rule was made in response to awareness that conflicts of interest such as these were undermining the integrity of research.

If the scientist did give all consulting fees to an academic organization that he founded, that doesn't mean he wasn't avid for more fees to make the organization bigger, or that he could not possibly have biased his research to get them.

Biasing research does not always mean lying. There are more subtle ways that involve fooling oneself. If he was convinced that the main causes of cancer were things that the victim had consumed, that too could have been a motive for bias in the same direction.

Wikipedia's article on vinyl chloride, as of 23 Feb 2017, footnotes a printed article from the Houston Chronicle that says chemical companies tried to manipulate research about the medical effects of vinyl chloride. When companies do this, they typically try many avenues of influence.