Something is very wrong with latest 1.12.2-1.3.1 version... Many drops are missed (from wheat for example), and also there are some strange "empty drops":

JEI 4.8.0.117 + JER 0.8.6

does the problem remains when you delete the blockdrops.txt?

Yes, it helps. All empty recipes are gone (probably its from currently disabled mods).
Never noticed that file, why it's exists and no auto-refreshing?