This I noticed.
This only happens when you reload a save game. even on my games the glow effect is there but seldom. there was a patch that messed this one up but I am not sure which one.
and also I mostly see the glow on weapons which inflict slash damage(sabres, swords, daggers). but its a known bug and it really removes the unique appearanc of the cipher.
what I did is that I exit the game, open steam, verify the game, play the game, reload the save game and there all the effects are back.
but if you reload a save game, its gone