zpool upgrade -V bumps the on disk version number, but leaves the in core version
zfs - Zettabyte File System
From John Kennedy's original bug report at Delphix:
To reproduce: zpool create -o version=5 data c2t1d0 zpool upgrade -V 9 data ...at this point, ::spa and zdb -C will say '5', while 'zpool upgrade' will say 9.
The problem is that the spa config is not being updated when the new version gets synced out.