It seems a layer of varnish added later to protect the work is in fact turning the yellow to a greyish-orange colour.
High-intensity X-ray studies found that compounds called oxalates were responsible for the colours becoming dull, the BBC News reported.
In 2011, an article from a team led by the University of Antwerp's Koen Janssens reported that a pigment Van Gogh favoured called chrome yellow degraded when other, chromium-containing pigments were present.
The new work was begun during a conservation treatment in 2009, when conservators found that the yellows in 'Flowers In A Blue Vase' - this time from a pigment called cadmium yellow - had turned greyish and cracked.
So the team again took tiny samples of the work to some of Europe's largest sources of X-rays.
The purpose was to determine not only what was in the samples in terms of atoms and molecules, but also the precise structures in the interface layer between the original paint and the varnish.
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The team found a compound called cadmium oxalate as the cause of the grey-orange pallor.
"The contact layer between the varnish and the paint, where the cadmium oxalate is found, is micrometre thin," Dr Janssens told the BBC.
"If we had not used methods that allow us to interrogate this very thin layer, we would never have noticed that there were oxalates there," Janssens added.
Oxalates are commonly found in much older works, and in association with different pigments. This is the first time that cadmium has been seen to form oxalates within the varnish - a protective measure that was added much later.
"Van Gogh didn't like to varnish his paintings - he liked them, let's say, rough," Janssens said.
"It was only after he died that these paintings found their way into the art market and into private and public collections and individual conservators would say 'we're going to varnish it because we do that with all our paintings'," Janssens added.
The particular chemical reaction may be putting the yellows of other works at risk by Van Gogh and others, but it does not happen with every type of varnish.
"I don't anticipate it will be a wide-scale problem for our particular collection, given its conservation history," said Ella Hendriks, the head of conservation for the Van Gogh Museum in the Netherlands.
"But of course it's always good to be aware of the possibility that you could come across this in other paintings," she said.
The findings were described in the journal Analytical Chemistry.