With the help of FIFA's Information Services department I managed to solve the June 2009 differences for England, Trinidad and Tobago, Greece and Armenia. Those differences involved two matches played on June 1st, 2008 (Armenia - Greece and Trinidad and Tobago - England). It had to do with the unofficial deadline used back then. I still have a one point difference for Japan, but will solve it in the near future.
With those problems fixed, England's ranking in the July 2009 preview drops from 6th to 7th, with Russia taking advantage of this. Armenia climb 5 places from 128th to 123rd.
The June 29th update will have the correct values.