Playing in a survival world, after both Taking Inventory and Getting Wood are unlocked, crafting a workbench or any achievement related tool (such as the pick-axe or sword) doesn't give the achievement. this happens both in the 2x2 crafting grid and 3x3 crafting grid. It is interesting to note that under Statistics, it doesn't record any crafting events but displays that I used them (screenshot attached).
Can confirm. Only happens when shift-clicking. Relates to MC-106030.