Upgrade to 1.5.6.1 duplicate modules + translations not working

[sshare]

Hi Everyone,

I upgraded from 1.5.0.17 to 1.5.6.1 and for some reason all of the modules in the main prestashop directory have copied themselves into my theme folder. So modules I have installed under the root/modules folder now also appear under root/themes/mytheme/modules

 

My translations also appear in the backoffice but they do not show on the front office, this affects all of my modules that normally have a version in the theme folder.

Is it normal for the modules to duplicate when upgrading to 1.5.6.1 I don't want to go deleting them and trying to fix it if in fact it's supposed to now be like this (which I doubt).

 

Also if anyone has seen this before please let me know how to fix it, as my idea to fix it is simply removing all those files from the root/themes/mytheme/modules folder and uploading the clean files in order to try and fix it.