This is because there hasn't been an update to CUDA to support Yosemite. If you look at Nvidia's official change log, you will see that 6.5.18 was released on September 19, more than a month ago. But the current driver probably was set to display that message on Yosemite installs, regardless if there is a valid update available or not. We just have to wait to there is an official release, until then the popup will come up on every reboot.