Functional Show Stopper comes as one parameter of 'Priority'. I know Show Stopper.. but what is Functional Show Stopper ? What kind of issues can be categorized under this ?
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This sounds like, to me, simply a "shop term", something someone came up with in a particular location or locale. A quick Google search didn't really find much of anything to categorize this term or define it in a global way.
So, a "show stopper", as I understand it, is a bug that makes the software product and/or feature being released critically unstable to the point that releasing it would cause the application and/or feature to be just a load of useless bits sitting on the hard drive. So, a "functional show stopper", while it might not totally trash the application, would mean that the bug gets in the way of the intended functionality in such a way that a particular function or feature does not meet requirements and is even un-usable in it's current state. It might not completely destabilize the application but it essentially will mean that the designated feature of the application might as well not be there.
I'd agree with Tristaan that "functional show stopper" sounds like a term that your organization uses for internal tracking purposes.
I'd suggest you start by asking people you're working with for a clarification of how you're expected to use the term. It could mean anything from "this function is unusable" to "this is a show-stopper bug that is triggered by a function" (compared to a "performance show-stopper" like "it takes half an hour to load the application and data entry is accepted at a rate of one character every two seconds") (Don't laugh - I've had to work with applications like that...)