I suspect this bug isn't a bug after all. My guess is that this was an intentional change left out of any patch notes simply because of the uproar it would cause. Much easier to slip it in and let a small minority of players bumble about on the forums trying to figure out what happened.
The reason I believe this "bug" is intentional is that without it ships that can cloak are able to circumvent some parts of missions, especially the parts that had us being surprised or ambushed. I regularly used my Defiant-R to cloak during the initial dialogs of the Deferi daily missions or Enemy Confrontations and that completely changed the dynamics of those encounters. It's probably much easier to railroad players down a set path now that they uncloak at every dialog.
I could be wrong, but the conspicuous lack of comment by the devs is suspicious. Regardless of what the Engineering Report says, I'll believe this is just a bug when it gets fixed. [/paranoidrant]