There's a major departure from how we understand backgammon to work.
Resignation has not been implemented in the standard way. Fencer didn't realise that resignation is a multiple-choice request that the "winner" accepts or rejects. Instead, we have a Brainking version that automatically decides whether it's a normal, gammon or backgammon loss depending on the postions of the men. If there's a man on the bar or in the winner's home table then it's a backgammon - regardless of how the winner's men are positioned. If the loser hasn't yet born off a men then it's a gammon. Otherwise it's a normal loss. There's no choice for the loser and hence no requirement for the winner to accept or reject. An example of how strange this is - if you resign when it's your first move then you will lose by a backgammon!
The result of this is that resigning is not an option unless you are going to lose by a gammon anyway. To have a normal single-point loss means having to play the game out until you've taken a man off the board. Only then can you resign a single.
I've spoken to Fencer and my feeling is that he's put a lot of effort into "The Bug" and into getting the BG+cube together and that adding a request-resign--accept/deny dialogue is one complication too far. As resignation is only a shortcut, it's not as serious as The Bug, ie it won't mean the wrong player losing, but it will extend games longer than otherwise or cause unwary players give away points that they needn't. Because of that last possibility, I've requested that the warning be highlighted in red or something.
(I'll add the short version of this issue into the list but thought it deserved a separate post)