I've recently installed a second HDD bay in my laptop, but now, every time I issue a reboot, the computer hangs for about 1m30s (completely freezes on a black screen, with the fans at the maximum rpm). From what I've been able to gather, this only happens when I have a HDD/SDD on the main SATA port on the laptop (originally used for HDD, now with a SSD mounted). With the SSD mounted on the secondary SATA port (and no HDD on the main port), reboot is normal (no hang, pretty fast).
This happens in both Ubuntu 12.04/12.10 (Linux kernel 3.5) or Arch Linux (kernel 3.7), but also when rebooting from live USB. Don't have Windows installed, can't say if it would also happen.
The strange thing is, this only happens when issuing a restart, not when shutting down.