I got that issue for two days. I created a file on photoshop cs6. It contains many layers, some of them are shape layers filled with gradient. I worked for few days into the file (by opening and saving it daily or more). But now, when I opened it, many gradient shape take a new color, the one on the color selector. Then, when my color selector is on a purple color when photoshop is started, the layers take a purple color (instead of blue as initially chosen, for example).
That issue only occured with gradient initially composed with foreground or background color. Not with other gradients.
Here is a print screen (the circle should be blue, but when I opend it with puprle selected, it appeared purple...)