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?