Surprised to not find a post on this but it seems that the “create all” profession button or putting more than one item into the scrapper breaks the profession / scrapper window which can only be fixed by a relog.
Hope this gets fixed soon as it really sucks to have to click a button hundreds of times instead of just afk crafting everything you need.
I submitted a bug report about this, and someone offered a solution.
Load one item at a time into the scrapper. Scrap it, then trigger a spell (like Cure Poison or something). Then load your next item, scrap it, trigger spell, rinse, repeat. It’s slow and tedious and annoying, but it’ll work.
I am having the same problem. If I try to craft more than one item, no matter what it is or how many, only one item will be crafted and then the operation stops.