yeah that menu closing automatically has been happening a lot for me a lot, especially when I try to loot my own body. I noticed if the whole body doesn't highlight, then the menu is going to be bugged and auto close.
I think this is effect of new looting system. They provide new mechanics on top of old mechanics and something was messed up. In 3.22 i had much less problems with looting.
Hey to anyone wondering, the bunker not existing is because the server isn't communicating the information (low server FPS). You can check it by pressing ` (next to the 1 key) and entering "r_displayinfo 1". It's an old issue and has been around forever. I have a couple thousand hours in SC and to be able to have any fun at all you have to know how to get around the bugs. Your inventory one was absolutely effed though.