making a stone pickaxe

I had 6 sticks for the handle and put 64 cobble for the head. The I shift click the output. I got 6 pickaxes as expected but then the cobble head part of the recipe remained and it thought to itself, oh he wants slabs, let's mass make those too. and now I got 72 slabs.

Expected result:
6 pickaxes and then I'd have to reconsider using the remaining cobble for something else.

similar thing happened with torches
had 4 sticks and put a stack of coal on top, got 16 torches and suddenly 56 coal dust.

mods in the pack i'm building:
http://paste.ubuntu.com/p/3d88r53yRx/

This is still present in 1.7.1 (at least in FTB Interactions 1.5.0)

The added checkMatrixChanges check at https://github.com/Shadows-of-Fire/FastWorkbench/blob/master/src/main/java/shadows/fastbench/gui/ContainerFastBench.java#L81 always evaluates to true because it is only ever called immediately after it is reset to true at https://github.com/Shadows-of-Fire/FastWorkbench/blob/master/src/main/java/shadows/fastbench/gui/ContainerFastBench.java#L135
thus, the CraftingManager is still queried for a matching recipe in all the cases it would have been before b145e90

Everything about your statement is wrong. The issue is not still present, nor do you even appear to understand how that method is called. The manual call I do there is not impacted, but the other (up to 576) calls are.