So before I updated to the newer version, No one could /msg me or /seen me. Now they can when I am vanished....and it is very frustrating!

That'd be an issue with the plugin providing /msg and /seen

well I haven't touched anything except updating vanishnopacket. Worked before the update.

What plugin provides your seen command?

I am assuming essentials, I figured out the /msg but, that was the essentials hook hide thing.

If you use the essentials hook it acts like you are using essential's /vanish as well, the /seen problem is because it doesn't actually log you out, it just displays a message that looks like you left