EE3 seems to be unable to create energy values for vanilla items when another mod adds an alternate recipe for the item (i.e. iron blocks) containing items that don't have an energy value. Could it be possible for it to default to the vanilla recipe? I'm not expecting a fix any time soon, as its early days and this issue only exists alongside other mods.

I would just like to add to the list of people having this exact problem!

This is likely due to people using the OreDictionary in funny ways. You can always set the correct values yourself in your instances using /ee3 set-energy-value