I think this is the same issue reported at http://www.dejal.com/forums/2016/05/27/breaks-not-resetting — if I've understood that one correctly — although I am using 2.1 and not 2.0.2.
The behavior I'm seeing is this:
1) I leave the computer.
2) I'm gone long enough for it to go to the lock screen and then go to sleep.
3) I return to the computer later — *much* longer than the duration of either type of break I have scheduled in Time Out.
4) A few minutes after I sit down again, Time Out starts a break — in some cases, a major break, before which it should've let me work for 50 minutes.
I too have the natural break detection method set to "Event Monitor".
Is there something I should try changing in the settings? I'm hoping I'm just missing something; clearly this isn't the app's intended behavior, right?
Re: Breaks occur right after returning to the computer
You could turn on the scheduler logging in the Advanced prefs, which will show what the app is doing in the Console (system.log if you're on Sierra).