DUE doesn't start properly after applying input voltage (dc/usb), have to reset

I have a problem with my DUE. It sometimes doesn't start the uploaded program after applying a voltage to the board. When it happens I have to push the "reset" button to start the program. It never happens if I unplug input voltage for a while and switch it on again after a couple a seconds but it won't start again if the switch_off_time is more than 10-15s. It's independant on what is the source of the input voltage - usb or dc_plug, no matter what i use, it behaves the same.

My board has C20 measured directly on the board ~30nF (10nF n the scheme). I have already solved the different problem with not-resetting properly the board while uploading - wrong value of R23, I've soldered 1k instead of original 10k.

Still don't know why sometimes DUE doesn't start the program after switching the voltage ON. I've seen others have the same problem but I cannot find the solution for it. Is there something like FUSES in the SAM uP to set a kind of "delay" for the system? I mean sth like 50-60ms?

I temporarily solved it modyfying ATmega16U2 firmware - now it does additional reset when the board starts.

What is more, I've "captured" kind of time-stamp-image of signals: reset, +5V, +3.3V using chineese Saleae Logic to see what is happening on these specific lines (I know, I know, oscilloscope would be better but here I have only "Salelalae a'la Logic"). And what? 5V line is starting as first, then reset line is going up....and then 3.3V. Interesting is that all these lines are "bouncing" a couple of times before getting stable (periods us). For example reset line (captured by "Saleae Logic") bounces 3-5 times - there is no direct and simple transition from "LOW" to "HIGH" , +5V line the same. It looks to me as a unstable voltage source - unstable before getting stable, maybe that is the purpose of stacking after applying fresh input voltage...reset manager gets crazy somehow...

Could you please point up or give your version of firmware? I have the same problem as well and right now don't know where to start.