Not sure of the cause, but in many cases JEI does not show most tools, with the exception of paxels, scepters, and katanas. Tested in 1.11.2, not sure if other versions are affected. This may be a JEI issue, as all tools show up correctly in creative menus.

The tools that do show are all subclasses of the vanilla tool types. Paxels extend pickaxes. Scepters and katanas extend swords.

Have tried (all without any effect):

• Removing the JEI handler in SG
• Not caching sub items list.
• Removing paxels (not registering them).

Fixed in recent versions.