This is my SECOND machine (same set up on the previous machine) that is experiencing these issues. Once I run the disk utility off of the original OS disk everything is fine.
Invest in a couple things - backup drive, Disk Warrior, and SuperDuper
Install OS X to part of your external (small and just big enough for an emergency system and minimal programs).
Booting off DVD is fine, but no Finder and you are limited to the (older) version of Disk Utility on there (and it does get updated and changed).
Clone your system for boot backup, especially before updates and changes.
Disk Warrior recognizes and repairs more issues, some of which Apple First Aid doesn't even look for.
So even though it appears okay afterward...
Next would be to run Apple Hardware Test, and along with that check your RAM with MEMTEST (REMBER is handy and is just GUI wrapper to memtest program) or run Memtest yourself from the Terminal.