So basically, this is the recipe for the Pulse Piston from FactoryTech that's displayed in JEI without adding a stage to it:

And it obviously works

This is the recipe displayed in JEI once a stage is added to it:

And it does not work

already fixed in dev, just released on curse

Actually, after further observation, all Shaped recipes seem to get displayed as Shapeless after they have a stage added to them.

This popped up again in 1.0.6. setRecipeStage() caused the recipe to appear shapeless.

JEI shows the Spindle recipe like

But that doesn't work and it actually is like