because there is a chance, that millis() returns something lower than 1000 and the next time something  higher than 1000.

here's how you could do it:

1. int timer = 0;
2. void setup() {
3. }
4. void draw() {
5.   // version 1
6.   if((millis()-timer) >= 1000) {
7.     println(frameRate);
8.     timer = millis();
9.   }
10.  
11.   // version 2
12.   //if (frameCount%1000 == 0)  //depending on the framerate
13.   //  println(frameRate); 
14. }

That's because when draw() is called, millis() is semi-random (intervals are not guaranteed). So the probability at it is an exact multiple of 1000 is rather low...
You might want instead if (frameCount % 60 == 0) println(frameRate); for example. You are sure that draw() is called on each frame, by definition.
[EDIT] Well, that's more or less what thomas advised, except that 1000 frames is a bit high!