If you are running on PC (Windows), make sure you are fully updated with the most recent patch. The way to tell the difference is that in the updated/recent patch, there is a live timer in the bottom right corner of the screen that will give an extremely accurate time to the millisecond. Outside of that, just make sure you enter your time with milliseconds and make sure you select the "new patch (with timer)" for the version when you submit.

Also: BE SURE TO ENABLE THE TIMER IN THE MENU. The new timer is not active by default, so you will need to check the box to enable the timer after downloading the new patch. After activating it, it will stay active each time you open the game, so you only need to do this the first time you download/open the new patch for the game.