It seems to related with Samba. ArchlinuxARM has same problem which use mainline kernel. I copy file from espressobin then it losses network connection, and I can't find any log.
This problem can be fixed by disabling networking service. However, you need to configure your network by other manager like systemd-networkd or NetworkManager.
Btw, can you check SD card is available in U-Boot after reboot with mainline kernel? My SD card can't be read by U-Boot after reboot. You can check the post here.