It's either because you have Vanguard installed twice and are using different locations for each, or due to file virtualisation. I'm not sure which file(s) you'll need to change until I check on my home computer.
Additional info:
The UI you will use depends on a line in the file VGClient.ini (ShellName=...).
I have vanguard installed in S:\Vanguard. You can check where Inner Space thinks Vanguard is by looking at your
Game Profile in Inner Space.
When I launch Vanguard outside Inner Space it uses S:\Vanguard\bin\VGClient.ini to decide which UI to use. But in my ISBoxer profile I
virtualise VGClient.ini so that each Character has their own settings. This is a good idea for Vanguard because this is the file that stores all your graphics and audio settings - doing so allows you to have different settings on master and slaves. That means that when I launch the Character Djur he uses the file VGClient_Djur.ini. This in turn means that if you change the UI in VGClient.ini it will not automatically be changed in the virtualised files - you will need to do that yourself.