Before switching from CS5 to CS6 I could overwrite files very usefully, but now the software often fails to overwrite saying "rendering error ...blah blah ...Unable to delete existing file etc."
Im using the same OS and method (the old cmd+optn+0 followed by cmd+shift+d - hit return ... relax ) but my happy days are now spent deleting the pesky files manually or building up a folder of useless incremental numbered files.
Might be QuickView is to blame. If the OS is displaying any preview of your file, even in Column view, it's considered "in use" and can't be deleted. Close all your Finder windows before rendering and you shouldn't have any more issues. At least that's what always hung me up. Now I do Cmd-Opt-W before I launch AE and haven't had a "can't delete existing file" failure since.
It is easier to destroy than to create.
More fun, too.
I'm using Windows 7, and I noticed this start to happen when I upgraded to Creative Cloud. The render error is "The file [path/filename] cannot be overwritten as it will be used for rendering." It seems to be this is a new dialogue that has been added to After Effects in recent upgrades. Not necessarily an issue with the OS. Unless the OP was having a different issue. But I haven't found a workaround for this particular dialogue box (other than to not overwrite a file that After Effects is currently using in the composition being rendered, turned off or not). But I do really wish Adobe would add some sort of option to turn this feature off and allow the files to be overwritten. It makes updating/overwriting proxies and pre-rendered comps difficult, as extra steps now need to be taken. OP, I feel your pain.