JanMalte - I would like to ask you all list of modifications which you did after re-flashing. And please send me your files

/etc/init.d/rcS
/etc/event.d/rcS-late
/sbin/preinit
/bootmenu.sh

I see the mount of uSD partition 3 as a swap before mounting eMMC partition 2 which should happen in /bootmenu.sh
Taking into account that swap mounts may happen in 2 scripts (rcS and rcS-late) which never run before /bootmenu.sh (it mounts EXT3!), I can't explain that.

It is a biggest issue for now. In normal boot it shows in log in regular place.

Can you check that your /var, /var/log are not symlinked to some place in /home? It can be a way how the same piece of log is duplicated in both logs. It is also very difficult to explain.

Can you also run EXT3 FS check? -

/sbin/fsck -n /dev/mmcblk0p2