You assumed incorrectly.

I killed xine and edited the file while xine was not running.

in fact the line gui.dropped_frames_warning:0 is now permanently in the config file but still I get the notifications (or at least some of them)

Nobody reading these lines knows what part of xine´s source code do I need to murder to get rid of the notifications once and for all ?

wrote:

...

I have added

gui.dropped_frames_warning:0

but still if the system gets stressed I get a warning box

Some xine dev knows by any chance how to remove xine?s ability to display warning boxes or to make them of size 0x0 pixels ?

I assume you did not unload xine before editing the config file. The file can not be edited while xine is running.