Update: it's happening to Iberian and Greek portrait characters too, now. Every time I make a clean-shaven Roman he is given a beard, and every time I give a Greek character one type of beard the game resets him to have a different beard entirely. Most annoyingly of course is that the bug resets itself: make a ruler designer'd character of Iberian, Greek or Russian graphical culture, customize his appearance, save then reload that save and the features you set will be changed. You can use the customizer to put them back the way you wanted them... but they'll change again the moment you save and reload, even if the character in question is long-dead.
There is a Conspiracy of the Beard afoot.
Edit: Changing your beard from one beard type to another then saving and loading resets the beard to what the game wants it to be. Changing your hair and beard at the same time saves the new hair type and occasionally the beard design, too, but more often than not the beard resets. You cannot set clean-shaven at all, that will always reset to a beard. Again, this only seens to happen with Iberian, Greek and Russian portraits - I tested and couldn't reproduce it with Western European portraits.
Edit 2: New discovery - on occasion, ruler designer-ing a Greek character with a beard... can result in a character without one. *crazed, choking, sobbing laughter*
