Hello,
Below is what I use. You need to have the modrewrite enabled if you are going to disallow index.php and even then it's still very risky. This may be part of the issue. Robots.txt is so important, but you need to know what you are doing. Especially when disallowing as much as that UK site is.
Tyler
User-agent: *
Disallow: /*?
Disallow: /*.js$
Disallow: /*.css$
Disallow: /checkout/
Disallow: /catalogsearch/
Disallow: /review/
Disallow: /app/
Disallow: /downloader/
Disallow: /images/
Disallow: /js/
Disallow: /lib/
Disallow: /media/
Disallow: /*.php$
Disallow: /pkginfo/
Disallow: /report/
Disallow: /skin/
Disallow: /var/
Disallow: /customer/
Disallow: /enable-cookies/
Sitemap: http://domain.com/sitemap.xml