@malveo, it looks like the following solves it,
EXTRA_IMAGECMD_ext4 = "-i 4096 -O ^64bit"
A deeper investigation is pending to understand this better, but it seems that on zeus branch 64bit feature is enabled by default and it seems that it re-writes meta data.
Edit: For additional context read https://tracker.mender.io/browse/MEN-3513 (in the end this fix was applied to zeus branch)