Try breaking and replacing the casting table itself; in my experience, it can bug out a little when you get to pylon casting and that usually fixes it. Also, the repeaters don't need to be in any particular order, no. However, a tip: placing 4 multi-aura repeaters a few blocks off the corners of your casting complex will make things a lot simpler, in the long run, as you just need to run your repeater lines to them, and not all the way to your casting structure. Its also good if you're like me and tend to build your ChC stuff relatively close together, so you can draw all colours from your network with minimal effort.