With the permission of Dean Sekulic of Croteam, I attach here his replies to my
e-mail message:

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I've just double checked and we definately set GL_DRAW_FRAMEBUFFER to 0
(default back buffer) before clear.
So wild guess would be that this is a driver issue...?!
Or I missed something. :/ 
[...]
Please do investigate, as I'm not 100% sure that we did everything correctly
from our side.
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Michel Dänzer and the others, what do you think about?