First question is if you copied measures and sensors with your BT. If no, you should do it. In general copy paste for BT should copy configuration as well. But those sensors should be places on proper hosts. So check if you have sensor group placed on each agent group that should have this configuration.
If yes, be sure that for java you’ve created hot sensor placement, or restart for .NET application.
If your BT’s are related on Request data, be sure that you have proper configuration of Java WebRequests sensor and same for .NET Ones. Sometimes you have to enable for example capturing of particular request header parameter etc.