That screenshot didn't actually show a connectivity issue, just a rendering one. For some reason, instead of heading down the right fork, the ley line decided to turn left, follow it all the way to the pylon, then jump back to the first repeater on the right of the fork. It would do the same thing every time I had more than one pylon of the same color connected to the network: travel down the wrong path, then make a super long jump for no discernible reason and continue normally.
Connecting >1 pylons of any given color doesn't seem to work anyway, because the network will always arbitrarily choose one of the pylons and never touch any of the others in my experience, even when one of the pylons is completely out of energy and another one is kitted out with 8 power crystals and is full.
That said, I found out the hard way that you can right click on a repeater with a chroma-wand-thing to see how many hops it takes to get to a pylon of the same color. Every connection trouble I had I eventually managed to trace back from the pylon by checking each repeater to see where the problem begins. Also, sometimes after a server crash, the network map doesn't get saved properly and you'll need to chunk load each repeater at least once to get it to fix itself.