This seems to be more of a visual glitch, but when the stack size is changed in a crafting module's GUI and the GUI is closed and re-opened, the stack size can sometimes (more often than not in my tests) revert to the 64 default value. However, the module will still act as if its previous value is still set. Clicking the button will immediately set both the visual and actual value to the new setting, however.

Thanks for reporting! Fix incoming!