I had this issue with my left controller before and somehow got it to work after like 100 tries and after feedback from Oculus Support pretty much just having me re-install everything. They obviously didn't know how to fix this exact problem. Now the problem is back after a firmware update. After the update my headset worked worked fine, but the controllers wouldn't come on. I sometimes have to pull the batteries and then put em back to get them to show up, but that didn't work this time. I went into pair them, and my right one failed. So now, this is what's going on. When I even touch my right controller, it blinks. 3 fast blinks, 3 fast blinks and 3 slow blinks and continues that pattern. When I go to pair devices, the left controller lights go off, I press the home and Y button until it blinks, let go and it pairs. Then comes the right controller. It's already blinking when pairing. When I press the home and b button, it fails. It then goes on to the headset where sometimes it fails and sometimes doesn't.
Update - I tried again when typing this up. When it came time to pair the right controller, I didn't touch any buttons on it. While it was still pairing, the light went solid. At that point, I closed down oculus. When I started it up again, I skipped the setup completely. Now it works. So there's the fix.
I'm curious what exactly that blinking sequence means on the controller and if there is a definitive way to fix it. I will ask support and update here if I find out.
One note in regards to the suggestions of reinstalling everything, that doesn't fix the issue with the actual controller which goes into this blinking state even when the headset isn't even plugged in. It's something with the controller itself that seems to get hung up. A reset of sorts would be great.