I agree with the absolute linking suggestions, but other issues may be at large and determining these may depend on your adeptness at trawling through/'deciphering' your scripting and htaccess files. I was a bit bewildered to see that the OP mentions the alive directory as his site and yet two other posters mention it in their signature, are you guys all working on the same site?
I think the key issue is that we know google has bugs with variations in urls and using the absolute url kills these bugs. Even if it doesn't help it can't hurt can it? to avoid this I use absolute urls and have the following in htaccess: Options +FollowSymLinks RewriteEngine on RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /index\.php3\ HTTP/ RewriteRule ^index\.php3$ http://www.domain.co.uk [R=301,L] RewriteCond %{HTTP_HOST} ^domain.co.uk RewriteRule (.*) http://www.domain.co.uk/$1 [R=301,L] Code (markup): mystik - I am 90% sure that its this issue thats causing your problems, I was posting the other day about google not being able to handle the trailing slash on Matt Cutts blog and similar issues can confuse google quite a lot.