A couple months ago, my MacBook Pro stopped booting reliably. It would just sit at the Apple screen and spin, sometimes all night. I could use the repair partition to re-install OS Mavericks and get back to work after a couple hours of downloading, installing, but it would get back to this bad behavior the next time I needed to reboot, which thankfully is not often. And safe mode booting didn't help same symptoms, so the problem wasn't in a cache known to safe mode.
I read on the support forums talk about the /var/folders directory which is used by the OS for some sort of caching. So this morning, when my son left my MacBook without its charger and drained it to the point of needing to reboot, I got another hang, and instead of two hours of reinstalling, I booted into the recovery partition, launched the Terminal app, cd into my normal boot partition, found the boot partition's /var/folders and deleted it.
And I then rebooted normally. So something in that folder is hanging up the boot process, I just don't know what.