Boot sequence prob's

Hi all I have a crucial M4 as my main boot drive and a samsung hd103 for storage. All has been fine until lately where upon on boot up the crucial is not recognized and the samsung takes over. When I go into bios the SSD which is connected to the 6Gb/s port is not there only the Samsung which is connected to 3Gb/s port. When I disconnect the Samsung and reboot the Crucial reappears, what I have done is set the Samsung to hot swappable so I can reconnect it after reboot so it appears in windows.

Hope it all makes sense and someone can help out.

Many thanks

Andrew