I created a little screen recording to show the effect on my mac.
There are no special applications running which would change the menubar (like Google Drive, ownCloud and the like)
During the video I am just surfing with Safari or clicking around in Finder on the other screen. This blinking takes place all the time. Sometimes it is colored, sometimes just bright or dark. It is really distracting when there's a blinking effect in the corner of your eye.
Any idea what triggers this strange behaviour? Or might this just be an annoying bug in Yosemite and I have to wait for an update from Apple?
(In the meantime I downgraded back to Mavericks using a TimeMachine backup, which - much to my surprise - was no hassle at all! I think I'll refrain from installing Yosemite again, until an update will be offered by Apple.)