You may want to remove the rim tape to inspect the spoke nipples/ spoke ends. Sometimes, especially with replaced spoke(s), the spoke(s) are just long enough to poke through the rim tape and be hazardous to the tube. If you find spoke end(s) poking above the top of the nipple, clip them or grind them down with a dremel. Then replace rim tape and remount the tire and tube to see if that solves the problem. When all other possibilities are exhausted, this is what I think of. Of course if you have deep section boxed/ aero wheels, the spoke would really have to be poking way above the spoke nipple, and it would be weird, as if the guy making the spokes chased them 3 times more than normal.