There is a small entry in the New Features guide that you would be forgiven for overlooking, it concerns a new property, 'Disable external references'. Innocuous enough but if you are struggling to get BIP to pick up your sub templates or maybe your BIP extension is now failing then this little property is the reason. It was introduced in 10.1.3.3 and essentially secures the XSLT engine and XML parser from accessing any external references, such as a sub template.
The property is actually called 'xdk-secure-io-mode' hence the title of the post in the configuration UI its called 'Disable External References'
It takes a boolean value - true meaning that the security is turned on and you can not access an external objects. So set it to false if you want access to your objects - it can be set at site and report levels.