Recipes have been broken after the last update (EnderIO-1.9.4-3.0.0.37_alpha), it can be fixed for singleplayer by deleting the config folder.
However it remains broken on servers.

What happened to the template and specifying exact version numbers?

Life happened

Do you know which parameters have changed between your old config and the new default config?

No I don't, both were default.

There's nothing in the config that could prevent our JEI handler from being registered.

However, I noticed it can take up to 2 minutes for JEI to process all recipes and recipe plugins. And that's with just Ender IO. So be sure to give it a moment or two before you give up. You can watch the client log, one of our recipe plugins spits out a message when it's running.

Okay maybe it was that 2 minutes thing, or maybe it fixed itself, I don't know, but now it works.