There has been a lot of changes in code for that update. Previously there was only index.php, now it was separated into many templates. So the English po file and po files are not having the same ‘location” for the words now.
Please kindly use that codestyling-localization plugin to regenerate the en_EN.po and en_EN.mo file and redo your translation.
Very sorry for causing these inconveniences.
By the way, this codestyling-localization plugin is a really good one, but does not know why it’s not available in WordPress plugins repository now.