I have the same problem. It looks like the flux profile is temporarily disabled. I have a dual GPU macbook pro, running Mavericks.
gfx.io shows that the GPU is in discrete mode all the time, while the flashing does occur. So I don't think the problem is caused by switching GPU's.
Automatic screen brightness adjustment is turned off. And thus the flashing also occurs when brightness is constant.
How could this be fixed? I'd love to use flux, but the flashing makes it unusable.