Preface

We have a number of sites that use the same redirect mechanism across the board. We recently transitioned one site from non-localised to localised and detected that the Google+ integration doesn't show up on the search results any more AND the PageRank is gone from 2 to 0.

How the redirect works

1. If the UA sends a cookie (e.g. lang=en), redirect the user to /language (e.g. /en)
2. If the UA is a bot (.*bot.*), redirect to /en
3. If the Accept-Language header contains a usable, non-English language, redirect to /language (English is the default on many browsers in non-English regions)
4. If there is a valid GeoIP lookup and the detected region is linked to a supported language, redirect to /language
5. Redirect to /en

We do of course on all pages have the proper markup to indicate the alternate language:

<link hreflang="de" href="/de" rel="alternate" />

As far as we can tell, we follow all publicly available guidelines from Google, so we are a bit at odds if this is a bug in Google or we have done something wrong.

Question

Does not having content on the root URL of a domain adversely affect search engine rankings and if yes, how does one implement a proper language redirection?