Just to test my theory, I bought a refurb 11" yesterday. I was looking to get one as a secondary machine anyway, but this conversation pushed me over the edge. It arrived this morning and I quickly changed the screen settings to the Macrumors colour profile that was doing the rounds for the LG screen. The screen looked 100 times better, but fundamentally, it made no difference, my eyes were still aching within about 10 minutes of using it, I then added f.lux to the mix to see if it would make a difference, and it didn't.
Just to clarify, I had an 11" previously with a Samsung screen, and this eye ache did not occur with that panel, at all. My eyes felt perfectly fine using it for any length of time. For reference, I have a 17" which has pretty much the same pixel density as the 11" and I do not suffer any vision problems when using it.
Needless to say, it's going back. I'm pretty convinced that there's something specifically about the LG screen that make some people's eyes wonky. It's definitely not everyone that suffers this, but for me it's a complete show-stopper.
Hopefully the 2012 models address this.