are you on windows? I find this happens on windows more so than mac. I believe its a combination of bad hinting combined with Microsoft's very crisp font smoothing. Windows can really mess with the kerning as well...
Fonts in Ubuntu can be absolutely unpredictable when it comes rendering time. I remember an install of msttcore-fonts that I thought would allow me to see sites built with Verdana, Tahoma, etc. similarly to Chrome on a windows box. Not even close, and I'm talking about the kerning, not even the subpixel quality.
IIRC as sibsib said windows takes major liberties with the kerning to keep its core fonts on the pixel grid, and if msttcore-fonts are hinted, they sure don't come out at all similar to the windows versions.
Not anymore. My fonts in Ubuntu are gorgeous and consistent everywhere except some Java applications, and even then Eclipse hasn't given me trouble for several releases of Ubuntu.
I know Mac users drool over their fonts, and as an owner and heavy user of my MBP, I much, much prefer Ubuntu's font rendering to OS X's and ClearType.
This is something very, very different. It's only on specific sites and it's only in Chrome when I have the hardware acceleration turned on.