This is starting to sound like something that came up a looong time ago, so just maybe... Try booting into another volume and running Disk Utility > Repair Disk on your disagreeable volume, and then reboot and see if your recalcitrant files are any more agreeable.

Last edited by artie505; 07/14/15 07:39 PM. Reason: Clarify
The new Great Equalizer is the SEND button.

In Memory of Harv: Those who can make you believe absurdities can make you commit atrocities. ~Voltaire