With version Quark-beta-29 for 1.9.4 and it appears that the ender watcher is uncraftable, I've looked in the changelogs to see if you changed something and nothing has come up.

Also two suggestions: Infinity II which can only be achieved with the tomes and allow you to use spectral and potion arrows infinitely. And maybe in addition to the lit redstone lamp have an inverted redstone lamp?

Did you change your config at all?