You've not said anything about how it actually shaves.
I don't think very many of the honemeisters here who have honed thousands of blades would say the HHT is definitive. Many razors shave well without passing the HHT. It's also true that after the 1K, the edge is still somewhat coarse and the "teeth" on the edge easily catch a hair. Smooth it out and make it sharper, it might just fail the HHT because, as one very experienced person suggested, the 1K HHT was a false positive.
It may be that you have a good, but coarse bevel at 1K, then on the Naniwa 3K you have sharpened the edge even more, but it's also smoothed out. Sharper, but without the "teeth" to catch the hair. Then the higher hones polish and smooth that sharp edge more so that it actually cuts the hair.
I seriously doubt the Naniwa 3K is messing up your edge.
Just my guess. Good luck!