Hi kalkov,
did a fresh installation, but had exactly the same result.
So I did another one and did some deeper examinations what happens in the different steps.
First, I checked the different partitions right after the upload of the installer. It seems to be that only partition1 and partition2 has any data in it. Partition3 and partition4 are completely empty.
I did the changes to config.txt in a linux pc as given by the screen manufacturer Makibes and did the first time boot in the RaspPi3.
It seems to be that the partition4 will be written during the first boot.
After that, I still got the wrong resolution. Therefore, I powered off the RPi again and mounted the card in my linux pc again. As I thought, partition4 is filled up but there is still no build.prop in the "system" folder in part4.
But then, after checking part2 again, I found that build.prop file in the root of part2.
Basically, there is no folder "system" that was my first attempt to search for that folder in all partitions. Due to I found it in part4, I concentrated on that folder first.
Now, after realising that the file is in part2, I did the changes to the config.txt file and changed in build.prop the force line into:
#from device/brcm/rpi3/system.prop
#
debug.drm.mode.auto=1
debug.drm.mode.force=1024x600
Wondering what "from device/brcm/rpi3/system.prop" does mean?
After umount and putting the card back in the RPi, I still have the mess that the resolution is not showing the full screen 🙁.
Moved it back in my pc and the file has been changed back to the former value 1280x720. Is there any automatism that is running during the start to identify the connected screen and using the 1280 value in case the screen is not known?
At the end I took a normal TV and connected the RPi to it. Then I was able to realize that the white screen at the beginning is a kind of initial setup. I ran through it having the hope that this has any positive effect and prevent any changes back to the 1280 value - no.
Moved the RPi back to the screen. Even after having a blue wallpaper now, and moved the power off icon to the upper left desktop to be able to clean shutdown the RPi, the resolution issue is still there.
The resolution is still not showing 1024x600. Every time after a booting the RPi and shutting it down again - now with the shutdown button, the build.prop file has no longer the value 1024x600.
Is there any kind of logfile that can be checked if there is any advice who or what is changing the value in build.prob back to the initial value? Does any script or service some changes to the file?
One other thing I observed during the boot, it seems to be that the OS needs up to 4 tries to boot until the first time the Emteria line painting (bootscreen) appears. It looks like, that the bootstep that brings the bootscreen runs 3 times and then in the next attempt, the bootscreen appears (read something like that in other posts as well - 
#78).
It reaches the last step before switching over to the bootscreen (something with kernel the last message say) and than the RPi reboot. At the fourth attempt, the boot succeeds and the bootscreen appears - but the painting is in the lower right corner - due to the resolution is wrong.
Hope that my typing isn't too long and forwards something usefull. In case you need more information of any file, please give me a note.
Cheers,
Garfield73
