Ok, I tried something new which seemed to solved the issue :
In my screen layout I have 5 zones or "Viewers".
One is playing flash slideshows as part of a "Scene" and the others are static images or text (some are scenes, other just an image of the right size)
Originally, some of the zones where just next to each other, with no extra pixel between them, and the swf zone had been created last so it had order 5 in the layout.
The two things I changed :
- Resized some of the zones so there is at least 5 pixels between them.
- Put the zone containing the scene with the swf in order 0.
The flickering is now gone (or at least is unoticeable).