If you haven't tried yet, re-pair your remote by following the steps below:
Remove the power cable from your Roku device, wait 5 seconds and then re-connect the power cable.
Wait until your Roku device displays the home screen.
Restart your remote. If your remote uses standard batteries, restart your remote by removing and reinserting the batteries. If your remote is rechargeable, press and hold the pairing button for 20 seconds. The status light should slowly flash green, stop, then flash rapidly. When this happens, release the pairing button and your remote has restarted.
Press and hold the pairing button for 5 seconds until you see the status light begin to flash. If the light does not flash, charge your remote or replace the batteries.
Wait for 30 seconds while the remote establishes a connection with your Roku device. Once the Roku device is connected to the remote, the pairing dialog should appear on your TV screen.