Possible commander display bug
I had the “same” issue.
In WvW (EB Map only), when I badged up it did not register. Even the Commander commands (/supplyinfo) did not work and said something like “You do not have access to commander features”.
It is fixed now, no idea wtf happened or how it fixed itself.
I did multiple restarts, entering/exiting WvW, badging on/off repeatly.
The fact that this happened is quite disturbing. And can sideline some of your best commanders if this happens to them, such as it did for me.