I'm going to take a guess and say that your rogue is pretty low level, right?
If that's the case, then everything is working as intended. By default (even in the original WoW UI) when your rogue goes into stealth your main action bar switches to another page, one that you can fill up with abilities that require stealth to be used such as CheapShot, Ambush, Sap, etc.
When your rogue isn't high enough to have a bunch of stealth only skills then you'll have an empty page 2 on your main bar. Then when you stealth it looks like all of your abilities disappeared even though your bar simply switched to the page with empty buttons. After your character is high enough to train some of the stealth only skills, run the mazzifier again and you'll find those placed on the second page and appear when you go into stealth.
I'll be honest with you though, this isn't something to be concerned about since honestly there's really not much point in even using stealth until you get an ability like ambush or cheapshot. The only useful thing stealth has until you get stealth required abilities is moving past mobs unnoticed.