On Jan 8 2007 Adam Lasnik of Google acknowledge a problem that Google has been having with root pages of .com’s that are hosted outside the US. Matt Cutts also of Google, also acknowledge the problem and described how it manifests itself (paragraph 8). In summary though, if you search "site:yourdomain.com" on Google.co.uk you will most likely get the root home page back in the search engine results page. However, try "site:yourdomain.com" on Google.co.uk with the radio button checked "pages from the UK" the root page is generally filtered out. This causes ranking issues if your home pages ranks for important keywords such as your brand on generic USP keyword. However, our belief is that the proportion of people using "pages from the UK" is small so traffic should no be greatly affected.
Our advice is to sit tight until EOP 17th of Jan. If problems still persists a comment on Matt Cutt's blog or at the Google Group thread would be advisable.