There's an issue in node (nodejs/node#12607) with submillisecond truncation of file mtimes on Windows, which makes yarns fileDatesEqual test fail on any file that's affected by the bug. This causes many identical files to appear changed causing unneeded re-copying on every yarn command.

You can run this to reproduce the issue:

var fs = require('fs');
var targetMTime = new Date('2017-04-08T17:59:38.008Z');

fs.writeFileSync("./file1", "");
fs.utimesSync("./file1", targetMTime, targetMTime);

var actualMTime = fs.statSync("./file1").mtime;

console.log(actualMTime); // 2017-04-08T17:59:38.007Z
console.log(actualMTime.getTime() === targetMTime.getTime()); // false

In my test projects this issue affects in the area of 10% of files, so in a project with 50000 files in node_modules you get roughly 5000 extra file copies per yarn command.