EP is per skill cycle in vanilla Glest, and inherently both engines, and has been
mentioned before. Basically, the produce skill goes through multiple skill cycles to produce that one unit. However, instead of consuming one bulk amount of EP as one would expect, it consumes the EP every cycle. Thus, if that produce command has to go through 200 skill cycles to produce that unit, it would need 400 EP. If the unit doesn't have enough EP, they can start the command, but won't get far before they run out and the command will be canceled (without refunding the EP). This applies to all cycling skills, morph, produce, build, etc.
If you want a useable EP on cycling skills, make a feature request, as it's not a bug. You'd need an entirely new XML element to avoid breaking past mods, but in the meantime, consider scrapping the usage of EP for produce, as it just causes serious confusion for both the AI and human players.