You seem to have a different issue than the OP (his remote doesnt flash at all)
Make sure you do NOT use the TV's USB ports to power your Roku (only use the supplied USB AC adapter).
1) Take the batteries out of your Roku remote
2) Reboot your Roku (remove and reinsert the USB cable)
3) When it gets to the pairing screen or Home screen, put the batteries back in (it should flash) and hold it inches away from the Roku until you seeing "Pairing Remote..."
4) If it doesnt pair within a minute, start over (you may need do this a few times)