What brand/type of string are you using? Is it Cobalts/NYXL/M-Steel by any chance? If yes, then maybe that's what is causing it. I had the same issue on a couple of Ibanez guitars where the sixth string (tuned to C) would do this kind of a pinging harmonic when chugging on the open string. The obvious workaround was using different string material. But since my guitar was equipped with the Edge/Edge Zero, stripping the winds on the saddle-side just enough to have the bit that locks into the saddle be only a plain string also solved the issue. Weird, I know but I literally pulled my hair out trying to solve this.