FYI, posting your machine model & specs & OS version might help with troubleshooting.....just a note for future reference
The next time you have the machine running, open system preferences, open the Start-up disk control panel, and select (highlight) the drive you want to boot from, then clik on the padlock at the lower left corner to lock it, and restart.......see what happens
if this doesn't help, you may have to trash the sud preference file, empty the trash, restart again, and redo the above step, and restart once more to verify....
if neither of the above works, then your HD may be almost full, or in the early stages of failure.