Unloaded WB 10.6 and Start Menu misalignments persist.
That looks like the default WB. If it is I have no problem with it. I did have a lineup situation with 1 out of many of the skins I made. Adjusted margins and all fine now. Other then that it is working fine on my win 10 machine. Have not tried it yet on my win 7.
The Diamond skin that a new Skinner may use as a template works fine also.
I would guess you rebooted after you installed the update. Sometimes as in the past when you loaded a WB it would be messed up here or there. Try loading another one and then loading the one you are showing again.