I have noticed when you have the hide recipes if missing research option enabled, after you make a new research JEI won't show the new recipes, but only after the player rejoins the world.
It does it the other way too - if i use command to revoke a research, the recipes will still appear till i rejoin.
Thaumcraft version: 6.1.BETA26
JEI version: 4.15.0.291
ThaumicJEI version: 1.6.0-27

I believe this is a duplicate of #34.