As SharePoint 2013 is making it way to the developers, solutions get upgraded to SharePoint 2013.
Thanks to Keith Tuomi, I will post the source of the problems here.
SharePoint 2013 offers the ability to be compatible with SharePoint 2010. In short, this means that a lot of features are ‘double’, one of which is the special reference in IIS to the _layouts folder.
In SharePoint 2013, the reference to the 15 hive is “_layouts/15” and NOT “_layouts”. Instead, “_layouts” points to the 14 hive.
In short, if you have resources and code relying on server side code and mappings, make sure you update the references to these files to point to the correct virtual directory!
Thanks to Keith for this information.