Hi hansibull,
Sorry for the delay, had some really busy time, and thanks again for helping me.
I tested now with enabled LTO and it works. I then disabled LTO and it stopped working and enabled/disabled (did this a few times) and it consistently works when I enable LTO and doesn't work if I disable LTO. So it seems this was the issue.
I also tried it the settings of 1Mhz, internal osscilator, and programmed the fuses to use internal osc and enabled CLK DIV8 and programmed the .hex with bootloader using Atmel ICE and Atmel Studio and it works as well.
I just searched on the internet to understand what LTO does and... I don't really understand, but anyway thanks for helping to identify how to make it work.
Kind regards,
Marius