I have this exact problem with one of my RT-AC66U routers. I currently have 2 of these connected in my home, one as the primary and one as an AP (Wired) for complete wireless coverage over my home. The primary router connected to my modem simply will not get the time sync'd, I have to manual...
I have recently been having a problem with my main router, I recently installed Merlin's FW 380.57 on ASUS RT-AC66U attempting to fix this problem but its the same result with stock FW (last 2 versions 3.0.0.4.378_9459 and 3.0.0.378_9533 same result)
I cannot get the NTP time to work on this...