I once had to kill the HL2.exe process to kill emp back when 2.0 first came out...the next time I started, settings were all messed up - console disabled, I forget what else, but it made the game near unplayable...and since there's no way to turn the console on in the settings....I take this to be a bug, since someone else just had it: http://forums.empiresmod.com/showthread.php?goto=newpost&t=4586
I think what happens here is that the config.cfg file becomes empty, and so the game reverts to engine defaults, instead of Empires defaults.