I think the code to make them save properly is still being worked on.
http://www.eqemulator.net/forums/showthread.php?t=25863
That fix wasn't put in, but there were some other fixes recently to correct many of the hair settings and other facial features I think. It probably still needs more work to make it so that beards save properly. Unless, you aren't using the latest code that has these fixes in it on the server you are having the problem on. I haven't tested it myself, really.