I first noticed this issue a few days ago so I don't know how long it's been there.
I'm using VanishNoPacket 1.8.8, Dynmap 0.28 and CB b1597, staff vanishes automatically on join (not on purpose, PEX doesn't like negative permissions) and are invisible on dynmap even when I disable dynmap hooking in the config file and they're visible ingame.
There are no errors in the console.

PEX is fine with negative permissions. You probably have the perm node vanish.hooks.dynmap.alwayshidden

Just negate the permissions you don't want as per http://dev.bukkit.org/server-mods/vanish/pages/permissions/

Several plugin authors have said negative permissions in PEX only work before the permission they're supposed to negate. For me they don't work either way, it might be because I use MySQL so the order in which the permissions are loaded is less predictable.

You should request support from the PEX folks. There should be a scenario where it definitely works.