I would report it as a GitHub issue with instructions how to repeat etc and get the core Engineers to have a look. Sounds like a bug on the surface... I would have a struggle describing why the mini cart being empty is a "feature".
Otherwise I wonder if what is happening is some context or cookie is not being maintained correctly between requests. I dont recall the details, but registered versus guest session tracking is a bit different.
Also there are different APIs for guest and registered user accounts. (The function calls take different arguments.) If mini cart got confused between the two modes and the wrong APIs were being used to add items to the cart, that might make a difference as well. Have you are doing any of your own code in this area, have you checked you are using the right API? Or that your calls have all the required arguments (being slightly different in some cases for guest vs registered user access)?
Did it work in 2.0 by the way? Some security aspects have been improved as well - it may be something permitted before has been closed as a potential security issue. (Again sorry, dredging up recollections from a patchy memory.)