Hey! I've been trying to get the companions to Stealth, however the normal stealth command while giving the "Your companion enters stealth mode" thing, does not make them enter stealth!
They seem to be treated as summons now, so this page might help: http://www.efupw.com/forums/showthread.php?t=64581&highlight=summon+commands
Maybe try typing:" /c astealth s or /c astealth h ", that may fix your problem.