I've been complaining for ages of awful metering on my X100, but after some serious testing today I've concluded that it's not the meter. The camera is simply not shooting at the exposure that it claims to be (I'm guessing the shutter itself isn't open for the duration it's supposed to be).
I put a big write-up with sample photos here. I put this all together to show Fuji and also so anyone with similar issues might find this post and know they're not alone!
If you have run into this yourself, please chime in in the comments below.
I found some other samples online and now know what the problem is. Scroll to the end of the main article; it's a stuck aperture. Ugh.