I fixed it, it was a power supply issue . I realized that my second HDD was very often unmounted/mounted by Windows (like it'd lost power) and that the bios boot process took more than the usual 3 seconds but like 10. I switched the PATA power cable and now everything is fine. I don't know why but the HDD problem somehow took some energy away from the video card (?? is that even possible?) and the VGA didn't have enough power to use the hardware acceleration, in fact i couldn't play h.264 videos with MPC HC and PowerDVD anymore with DVXA (I saw this today, that's when I got the power idea).
Hope would be helpful for someone