The flags and arms of the university and its colleges are illustrated here. The presidential flag is in use in this photo during a speech by Clinton.
Stanford University is large, private research university in the Bay Area of California, near Palo Alto.
The flags of the schools are banners of their arms. Comparing this photo of actual flags with the artwork given for each BoA we can see that the shades of red and of purple in actual use are brighter than depicted. Also noteworthy from that photo is the use of plain yellow and white for the heraldic metals, and the unusually light and bright shades used for green and blue.
No indication of these colors being used in any flag.
The flags aren't actually the banners of arms, but are derived from the blazons of coats of arms, which are also given here, but with no images. Consequently, all images may be made in couples - one for the shield of arms and the other for the flag.
Such derivations may seem odd, but are not unknown - in Serbia, a typical way to create the flag of a local government area is to simplify and re-arrange the charges of its coat of arms. This is done especially if the blazon is complex, while the simpler blazons are usually converted into the banners of arms.