Rather than ask a dozen different questions regarding your system, would you be willing to try the following?
Apple Support Communities contributor etresoft wrote a very useful app to quickly gather certain system information that may help point to a cause of this problem. Go to his website, download and run EtreCheck:
http://www.etresoft.com/etrecheck
Don't be concerned about anything that says "Problem" or "failed".
Copy and paste its output in a reply.
Etrecheck was designed to remove any personal information (such as your computer's name and serial numbers) but if you see anything that looks like an email address or any other personal information that should not be divulged to others, please delete or obscure that information when you post the reply.
When you are finished with EtreCheck, quit the program. It occupies very little space, and you can keep it or drag it to the Trash as you wish.
You should also boot OS X Recovery and use Disk Utility to verify and repair your disk if necessary. Disk corruption or pending failure could explain this.