I could probably fix this in the next update, but It would need to be tested.
If I set the game to pause every time a message box is opened, I would have to set the game to also un-pause as well, which could be problematic if you're in a menu activating stuff and suddenly the game is un-paused while you're still in the inventory.
I'll look into it, of course I always meant for the game to "keep going" while you were in menus. In the first few versions of the game, there was never a pause at any time, even when looking at menus and such. it was an idea I took from dark souls, that the world wasn't going to stop and wait for you.