The symptom you describe of having a hot pulse then weak pulses and again at some point later a hot pulse is the exact description of what I had going on with my fence a few years ago. The pulse energy on my fence tester went in a repeating cycle; a good hot 10kv pulse, then a couple weak ones, then nothing, then a good hot 10kv again, and repeat. I even had a buddy, who farms, has electric fences, and happens to be an electrical engineer come over. We tested the battery, energizer, ground, all good. It turned out, on my fence, the bottom poly wire had slipped off the fiberglass post and was barely touching the metal spike in the soil. I shimmied it off the metal post spike and back onto the fiberglass post, and problem solved.
If I read everything correctly, it sounds like your grounding, 8' high main hot wire and energizer are all working properly, and problems only occur when lower strands are connected. I suspect either something is unknowingly being grounded somewhere, or, one of the switches or disconnects is functioning poorly and not allowing the hot pulse to get through to the other side of the switch. The other thing that comes to my mind is 6 joules is not enough. It may be plenty for the main hot wire, and is why when it's tested it shows a good zap, but adding more and more conductor weakens the pulse.