We think the black wire carries the current for the SWG (among other things), though I'm not sure it's the hot wire. In DC wiring, red is usually the hot wire (which only matters for the point I make below). Someone here had heard from Pentair that they were going to address this problem by discouraging (somehow?) the use of the IC60 with the IntellipH. That led us to believe the lesser amperage requirement of the IC40 and IC20 is not sufficient to melt the connection. We now know that's not true in all situations. If it is in fact the current draw of the IC causing the problem, then that current is likely running through the black wire (but maybe not only that one wire, read on).
For a while, I think you should check on that connection periodically. I think it's possible that another wire could fail. It follows that if X amount of current was traveling through that black wire, then all or some of that current is traveling back out through one of the others. It's also possible that the current splits up and travels out through more than one wire, but I think its possible that most of it is traveling out through just one. I suspect the red one, for two reasons. If you look very closely at the pic that I modified, it looks a bit like the pin just to the right of the fried one has similar tinging on it. It's very vague, and maybe not there, but that is the red wire pin. If I was engineering this thing, and was coming up with the color scheme, I would run primary power through the red and black wires. Black would be common and/or negative, and red would be the positive DC wire to the SWG. In other Pentair four-wire connections, the red and black are power, and the other two are signal wires, so that might be Pentair's color scheme. So...
It's possible that the black wire (the common wire) had the most amps running through it, and the red wire had the second most. The black wire's pin connections acted a bit like a fuse. It burned out first (like a fuse would), because it had the most amps running through it. But now that you've bypassed the pins, you've eliminated that "fuse." Which might subject the next in line to be the next fuse. This is all very obscure, and maybe not likely. But it's worth keeping an eye on. Obviously that connector is inadequate for the current running through it. It's not a given that only the black wire is running too much current.
Anywho... thanks for pursuing this. You may have proven the workaround for others. We'll look forward to your future reports. Whoever did that work for you did a first rate job. And you've now provided the model for the fix.