The role instance does not report Ready until the OnStart method finishes and the Run method begins. You can validate this by looking at the guest agent logs on the VM itself (see http://blogs.msdn.com/b/kwill/archive/2013/08/09/windows-azure-paas-compute-diagnostics-data.aspx for more info about those logs).
When you access the endpoints are you waiting for response or just sending a request? See Azure Autoscale Restarts Running Instances for code which hits the endpoints and waits in OnStart for responses before moving the instance to the Ready state.