I have this problem in Chrome as well. You can read my comments on this thread, Master password reprompt not working - #7 by Joe_G
I’ve had to disable auto-fill to sidestep this annoyance. My desired behavior is to auto-fill when re-prompt isn’t required, and to allow me to select the account and input master password when re-prompt is required. Basically, exactly as it worked before. To the extent that a pop-out window is somehow needed for the re-prompt now, then it should be asking me which of the multiple accounts I have for a page that I want to use; and, most importantly, not incessantly launching that pop-out window.