Somebody please explain! Why X-E1 JPEGS are darker?

Viking89 is close to the right answer. However, he's wrong in suggesting that you would need to process from Raw to tell the real difference - ISO is based on JPEG output.

In our review of the X-Pro1 we found the X-Pro1 produces darker images than you would expect at any given ISO (it over-stated ISO by around 1/2 a stop). And that's the answer to your question. It's very unusual for modern cameras to under-state ISO, but the X-Pro1 is one of them - it appears the X-E1 does the same.

Richard - dpreview.com