It is likely too many redirects to one page (homepage). G seems to see this as a bit suspect though to the webmaster it is trying not to lose the accumulated equity.
If I'm not mistaken, Google does not like it when you redirect a very large number of pages to one. In their eyes, it may look like you are trying to funnel PR to one page.
Millions of pages? 301 to the home page? Ya, Google doesn't like that at all.
Specifically, look for possibly artificial or unnatural links pointing to your site that could be intended to manipulate PageRank. Examples of unnatural linking could include buying links to pass PageRank or participating in link schemes.
But, the message above is not related to the redirects. Google is telling you that it doesn't like your link profile. Although, the redirect could have triggered this. The links to the host name are now being counted towards the root. Remember, host names are treated a little differently. I'll bet that host name had its own link profile and now with the 301, it is becoming part of the root link profile. Maybe?