This error can be ignored as it is not related to the features you are implementing. The message occurs when a connection to a device that was set up in the Push Review to Device window is lost. You'll likely just need to reconnect the device when you're ready to review.
As for the issues you're having with jump links and popups can be due to several things so without seeing your files it will be difficult to narrow down. Can you provide me with a couple of the InDesign files you're having trouble with?