Could be a human thing, I have noticed something similar when using plasma tv to watch non-hd tv channels and hd channels. The HD channels caused more strain than the non-HD.
I think I was focusing differently when watching HD content, as my eyes were trying to pick out specific details, whereas they were more relaxed with the lower detail content. I think my issue with this plasma tv was ultimately caused by it flickering, but focusing more acutely may have aggravated it.
Of course all conjecture, I don't really know.