n00b1 - 9:31 am on Jul 24, 2012 (gmt 0)
It is a bit ambiguous really. You could interpret it as meaning that "they are taking targeted action on the unnatural links" which simply means devaluing them. The "instead of your site as a whole" is probably just to reaffirm that this isn't a penalty which does usually affect the entire site - it doesn't necessarily mean that it is narrower penalty.
If you follow what Matt C has said on G+ and elsewhere he seems to imply that the message is an FYI and it may not require any intervention from the webmaster. They even got rid of the yellow caution symbol to reflect that.