With BW&T enabled, selecting a transmog set that's saved only with BW&T (as opposed to the 20 default ones) at the transmogrifier never loads the appearances for your 2nd weapon as Fury or the weapon enchant on either weapon, it just remains as whatever the last selected set was.

Speaking of last selected set, it's never saved by BW&T (maybe related to the Fury weapon bug?), so every time I open the transmogrifier with BW&T enabled, it selects and applies the last transmog set that I used with the Blizzard interface, not the last set I applied with BW&T.