Here is a video of the problem:
http://www.dailymotion.com/video/x48cuc_strange-portal-behavior_videogames
Here's another version in slow motion where you can see the problem clearly :
http://www.dailymotion.com/video/x48dai_strange-portal-behavior-slow-motion_videogames

As you can see, when I'm sucked by the blue portal on the floor, I'm literally passing through the floor of the platform, without even touching the portal in itself. It only does that with these little platforms I'm making with func_brush entities. Does anyone have a theory and/or a solution ?

I've noticed similar behavior, though in your video it appears that the very bottom of the portal does get far enough under you that you'd fall through.

My first suggestion would be to try adding some player clip brushes in the platform near the edges (though I'm not sure how the portal would treat them). If that doesn't work you could always expand the size of the platform or surround it with a non-portal-able surface like the metal floor or walls. If you do add non-portal-able surfaces around the platform, be sure to put some func_portal_bumper's around the portal space.

Corion wrote:
I've noticed similar behavior, though in your video it appears that the very bottom of the portal does get far enough under you that you'd fall through.

No, I don't touch the blue portal, and I can't get much farther from it, because I'm already on the edge of the platform. But if you look carefuly at the end of the video, you see that I'm leaving the orange portal passing though the floor of the main room, and landing next to the portal. I was immobile when I was sucked by the blue one, so I should have passed from one to another indefinitely if the blue portal was really under me.

Corion wrote:
If that doesn't work you could always expand the size of the platform

No, I can't expand its size, because it's made to fit in an environment of 128x128 platforms. There's already a lot of things done before this part, and I don't want to change everything in the middle of the puzzle.

I'll try your ideas tomorrow, but I'm not quite convinced. The player clip texture does not affect portals and I can't surround the platform with non-portal-able surfaces, 'cause I can't expand its size.

Here's another version in slow motion where you can see the problem clearly :
http://www.dailymotion.com/video/x48dai_strange-portal-behavior-slow-motion_videogames
(added to the first subject too)

Ok, triple post, but I managed to do a workaround.
The problem comes from the fact that the platform is a func_brush parented to a moving object (func_door). Although there is a "Solid BSP" field (Set this if this brush is in hierarchy with a moving object of some kind, and the player can stand on this brush) in this entity, it does absolutely nothing in our case.
So, the solution I found is to make another func_brush, about the same size as the platform, textured with player clip and parented to the platform itself (and not the moving object, in my case, the func_door). Then, it seems that the problem just disappears.
Strange but, well... I'm kinda used to strange things with Hammer.