The new SHIELD Android TV has just launched with a smaller chassis, revamped controller, and a few new software tricks. One trick no one much cared for was the one where the remote would just stop working. NVIDIA says it's addressed this bug in the latest update.
NVIDIA made some changes to the remote this time around. It's Bluetooth now, and uses coin cell batteries that are good for about a year. It does this by going into sleep mode when you're not holding it. Perhaps this is the source of the non-responsive bug. The remote simply stops responding to presses sometimes. David experienced this with his review unit.
The update will have version number 5.0.1 and should be available for download now. It has "general stability and performance enhancements" including the remote fix. After installing the system update, you should have an update to install on the accessories.