Forge 43.2.8
FastWorkbench 1.19.2-7.1.0
Placebo 1.19.2-7.1.7

Set:
B:"Remove Recipe Book Button"=false
in fastbench.cfg.

Create new world.

/give @p minecraft:crafting_table
/give @p minecraft:cobblestone 64

Attempt 1: Add cobblestone to crafting grid sufficient for two furnaces. Do not use recipe book (doesn't matter if you are displaying it or not). Shift click to craft all.
Result 1: Receive 2 furnaces

Attempt 2: Display recipe book. Click furnace once to add cobblestone for one furnace, then manually add cobblestone for second furnace. Shift click to craft all.
Result 2: Receive 2 furnaces

Attempt 3: Display recipe book. Manually add cobblestone for one furnace. Click on furnace in recipe book to add cobblestone for second furnace. Shift click to craft all.
Result 3: No crafting performed

Attempt 4: Display recipe book. Click furnace in recipe book twice to add cobblestone for two furnaces. Shift click to craft all.
Result 4: No crafting performed

Attempt 5: Display recipe book. Click furnace in recipe book once to add cobblestone for a single furnace. Do not add any more cobblestone. Shift click to craft all (still only crafting one furnace).
Result 5: Receive 1 furnace

Attempt 6: Display recipe book. Click furnace once to add cobblestone for one furnace, then manually add cobblestone for second furnace. Click furnace in recipe book again to add cobblestone for third furnace. Shift click to craft all.
Result 6: No crafting performed

Attempt 7: Display recipe book. Add cobblestone for one furnace (whether through clicking furnace in recipe book or manually). Click furnace in recipe book to add cobblestone for second furnace. Manually add cobblestone for third furnace. Shift click to craft all.
Result 7: No crafting performed

Attempt 8: Display recipe book. Click furnace in recipe book twice to add cobblestone for two furnaces. Right click one of the stacks of 2 in the grid to remove only one of the cobblestone (the furnace in the output should not disappear). Manually add the cobblestone back, making the grid capable of crafting two furnaces again. Shift click to craft all
Result 8: No crafting performed

Attempt 9: Display recipe book. Click furnace in recipe book twice to add cobblestone for two furnaces. Remove one of the stacks of 2 in the grid (the furnace in the output should disappear). Add the stack of 2 cobblestone back into place (the furnace should again appear in the output). Shift click to craft all
Result 9: Receive 2 furnaces

So it appears that once the recipe book is used to add sufficient ingredients to craft multiple items, the output item is now "tainted" somehow and will not respond correctly to a shift click to craft all. Breaking up the recipe in the grid so that the output item is "recreated" appears to fix the issue.

Sorry about the edits but each time I started to write a summary I thought of an additional test and how I should edit the title.

Also, this does not occur with FastWorkbench 1.19.2-7.0.1