1. 1st I should point out that there is a vibration in the tubing, as well as a temperature difference, which indicates that there is at least SOME flow.
2. 2nd you said that the problem started after you reapplied the TIM. could it be a problem in the TIM/ water block mounting?
Did your machine work with a new cooler? I just got a new TR 3960x - the new one. It's overheating and shutting down. I used a Corsair H115i, which is on the list of AMD recommended coolers. When I first built the machine it started up and I was able to install windows 10. Then, after about an hour where I wasn't running any apps, the machine shut down. I've ordered an air cooler (Wraithripper) to try another cooler and see if that's the problem.
Just curious if a new cooler worked for you and which one you went with?
I went with "Noctua NH-U14S TR4-SP3 premium-grade 140mm CPU cooler for AMD TR4/SP3" and so far its been working great, i feel the unit I got earlier was faulty from the start, because the new Noctua does much better job than water cooler Enermax Liqtech TR4 360. Temp stays between 40-50 C most of the time. Though to tell you the truth, I rarely stress the system anymore like I used to.