Update: I've discovered that when starting Krfb without any other program interaction, right clicking and choosing quit in the menu I get the confirmation dialogue and it closes normally. But, if I start Krfb then choose restore in the menu to get the main window then close it and try and quit Krfb this problem occurs. Turns out that it's the dialogue window that is flashing up briefly.
Update: I've discovered that when starting Krfb without any other program interaction, right clicking and choosing quit in the menu I get the confirmation dialogue and it closes normally. But, if I start Krfb then choose restore in the menu to get the main window then close it and try and quit Krfb this problem occurs. Turns out that it's the dialogue window that is flashing up briefly.