i am running minecraft 1.2.5, ic2 v1.95b, and buildcraft 2.2.14
when i load my world, return from a distant trip or the nether, none of my batboxes, mfe's or mfsu's output energy. this requires me to destroy the first wire and replace it in order to start eu moving down the line again. however, i have batboxes outputting directly into batboxes, which requires me to remove and replace the whole box before the adjacent box will discharge.
i used to see this problem only with the reactors(as far as ic was concerned), which required a similar change for the same conditions, i have not confirmed that the issue exists in 1.95b yet as i have not constructed a reactor as of yet. i noticed that the reactors did not have this issue if they were not running when they were loaded into the map.
i also saw this issue on buildcraft's transport pipes until the latest release. (i know you don't support buildcraft, but might ask them how they fixed it?)
if this is in the wrong section, please feel free to move/rename it.