indyank - 10:04 am on Aug 30, 2011 (gmt 0)
The strength of the sitewide drag depends on the quality score. This algo is probably evaluating signals from a sample number of pages in a site, for the "google quality factors". When the quality score for the evaluated sample is moderate, the corresponding site wide drag will be moderate ad if it is poor the site wide drag will be stronger.
Splitting to sub domains with fewer pages is probably limiting this damage.