Browser caches might need cleared as well. If you have it working in one instance, then at least you know that the site is ok.
Yesterday I decided to upgrade Moodle to 2.9.3 in order to try to fix the problem. Upgrading went well but I got a warning:
unsupported_db_table_row_format:
Your database has tables using Antelope as the file format. You are recommended to convert the tables to the Barracuda file format. See the documentation Administration via command line for details of a tool for converting InnoDB tables to Barracuda.
Could that be related with the css problems?JavaScript is either turned off or broken. For the latter it could be anything. Press F12, look at the console, reload the page, look for errors.
Thanks Gareth.
I checked the source code and I realized some of it was missing (YUI library). After some research I desaibled mod_pagespeed module and it looks like it's working now.