You can try resetting the PRAM by holding CMD+OPT+P+R during boot. Let it reboot and chime three times (just to make sure) before letting go of the key combination.
If you want to get down and dirty, you can see if the console logs hold any leads. The log viewer is in Applications > Utilities, IIRC.
Also, do a check on your boot volume by booting into your recovery volume, opening Disk Utility from the list, selecting your OS X from the list, and running Repair Disk on it. If you're in Mavericks or earlier, you can hold OPT key on boot to get To Recovery volume. On Yosemite, hold CMD+R during power up to boot to recovery volume.
Hope this helps.