If you have the mobile app on your phone, use your phone to navigate on the left hand column to: SETTINGS > REMOTE > PAIR REMOTE and then follow the instructions listed on the remote pairing page. I was experiencing the same problem, and this solved it. Here is a link to the Roku Remote App For Android which I used to solve the problem: https://play.google.com/store/apps/details?id=com.roku.remote&hl=en_US
If your remote won't pair, try turning off your WiFi while you pair it. The remote uses WiFi frequencies and suffers from interference from the Wifi. I have to do this every time I go through the pairing process, but it does work every time.
This worked! Had the flashing green light. Went to settings, changed setting of wifi to wired. It rebooted and when it came back up it said it paired! Went to setting and put it back to wifi.