atime is not set when passing a Date as the documentation says

[aalexgabi]

In onopen:

  onopen (er, fd) {
    if (er) {
      if (er.code === 'EISDIR')
        this.onopen(null, null)
      else if (er.code === 'ENOENT' && this.nocreate)
        this.emit('done')
      else
        this.emit('error', er)
    } else {
      this.fd = fd
      if (this.ref)
        this.statref()
      else if (!this.atime || !this.mtime)
        this.fstat()
      else
        this.futimes()
    }
  }

In onfstat:

  onfstat (st) {
    if (typeof this.atime !== 'number')
      this.atime = parseInt(st.atime.getTime()/1000, 10)

    if (typeof this.mtime !== 'number')
      this.mtime = parseInt(st.mtime.getTime()/1000, 10)

    this.futimes()
  }

If atime or mtime is missing stat is called:

      else if (!this.atime || !this.mtime)
        this.fstat()

In the stat callback onstat if atime is not number it is overwritten with the value returned by stat:

    if (typeof this.atime !== 'number')
      this.atime = parseInt(st.atime.getTime()/1000, 10)

The doc says atime should be a date not a number

atime like touch -a Can be either a Boolean, or a Date.

The doc is wrong but this causes a bug that is hard to debug.