Apologies for the thread necromancy but I was running into a similar problem as the OP using EmulationStation on Windows; emulators weren't launching for some reason even though they worked fine when I ran them manually. I found this thread and tried making sure I was using full paths & %ROM_RAW% and etc., and the emulators still just weren't launching. I was just about to give up when, when I had the thought that perhaps the space in the directory name my emulators were in might be mucking things up and sure enough--I renamed the directory without a space and everything worked! I wanted to add to this thread in case anyone else came along hitting the same brick wall, hope it helps.
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