[Yrkoon]

I have that problem too. I noticed that the GUI disappears ONLY when I have a look at a commander (I rename a lot of them) from the main map, then go back to the main map again. I doesn't always happen, but every 2-5 turn is a good approximation.

There is a easy fix to this, at least in my case : I don't look at the commanders from the main map. Instead, I open the army setup for the province where the commander is (shortcut : t) and I look at the commander from there. The GUI never disappears when I close the army setup.

So to sum up:

Main map -> Commander view -> Main map : GUI disappears
Main map -> Army setup -> Commander view -> Army setup -> Main map : No problem at all

I hope this works for you.