Sometimes the crafting module has one of each ingredient item, satisfying the recipe, but it doesn't output anything. It's a rare occurrence, but the only way to get it working again is to open and close the module interface and/or update the GUI in some way, such as editing the stack size.

I now have a large autocrafting setup using separate sections for each stage in the complex craft I'm working on. Each stage has (ender) chests with the 3-4 raw materials needed and a chest for the output. The ingredient chests have a multi module, a filter module (set to that specific ingredient item), and an extraction module. Then there's the crafting module, and finally a supplier module on the output chest to prevent over-crafting.

With this setup at every level of the craft, none of the (ender) chests are ever completely full (thanks to the supplier modules) so there's always room for overflow to return and nothing ever gets stuffed. The bug might (I'm not yet sure because it is fairly rare) be caused by the output chest reaching its maximum and its supplier module ceasing to be a valid destination at or around the same moment a craft is ready to be output. If so, something about that condition prevents the crafter from resuming when the supplier is once again ready to flow. (There may also have been a server reset between those events, in at least one case.)

Let me know if I can help with this one more. I'm really liking this system for autocrafting, despite the couple of bugs I've reported. Without AE2, it's the next best thing.

Since posting this bug, I have not been able to duplicate it, despite running a massive autocrafting system non-stop using this setup. It may have been a fluke or a server issue. :/