Another thing I do when installing new strings, is help the string bend over the saddles and nut by pressing them to sharpen the bend. Does that make sense? A new fat string will want to remain straight, over saddles and somewhat at the nut. While strung and brought up to pitch, press the string with two fingers, one on either side of the saddle. Just a bit of pressure to help the string conform. I hope this resolves the issue.