I'm not sure if this is a bug, and I am in 1.0.0 still, but the EMC for redstone blocks, gold blocks, pistons, and various other blocks have no EMC value. I have noticed that Essentialcraft has gems that pop in as being oredictionaried, maybe that is a problem?
I mean pistons, really?
What I think is going on is that EMC values are hard coded for a few things, then the rest are supposed to be calculated based on their crafting recipes. That process only works when all of the items used in the recipes for a particular end product have EMC values. The example I noticed was vanilla books and paper. You'd think those should get EMC values, but they didn't get calculated for me.
Sugar cane and leather both have EMC values, and in vanilla that's enough for paper and books to get their EMC values calculated. The problem was that there's an alternate recipe for paper using Hemp, and Hemp didn't have an EMC value set. Since Hemp didn't have an EMC value, paper didn't get one either. Since Paper didn't have an EMC value, books didn't get one. Once I manually added an EMC value for Hemp and restarted the game, I got calculated EMC values for both paper and books. (I think I also assigned an EMC value to sawdust since there's a sawdust to paper recipe too).
My guess is that something similar is going on with your examples. It seems like once we get EMC values assigned for a few dozen basic materials added by various mods, most of the rest of the EMC values will fall into place.
There seem to be some other EE3 oddities, too. For instance, with my paper and books, they DID have EMC values at one point, without me doing anything. I know that's true, because I was able to scan them into my alchemy book thing, then the next day I wasn't able to pull them out of a transmutation tablet because they'd lost their EMC values somehow.