On the few occasions I've tried using secure empty trash, it takes forever (I hear this is normal) but when it's in progress it counts the number of items to delete incorrectly. I put one file in the trash, secure empty it, and it shows a progress bar stating that 5 items still need to be deleted. It was a large file, so maybe it's split into 5 parts? Or are there some other hidden files associated with my file that are being deleted as well?
Secure Empty Trash can’t count
snow leopardtrash
Related Solutions
A program that is accessing files in the Trash that you're trying to Empty could interfere with attempt to Empty Trash.
The resulting timeout causes the "Stopping…" (which takes forever) alert message that you saw.
You can turn off Time Machine and try again or perhaps reboot (after turning off Time Machine) and see if the trash empties properly before starting up Time Machine or whatever other programs might have files open.
A quick google found this article. You can enable secure empty trash as the default from the Finder preferences:
For nearly every version of Mac OS X, there is also an option to always securely empty the Trash, enabled within the Advanced Finder preferences. If you regularly work with private data this is a good feature to turn on.
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Best Answer
Secure emptying takes long because instead of marking the areas of your disk which stored the files you're deleting as "available", it overwrites them with junk in order to make difficult recovering those data.
What you say happens to me too, I think it's pretty normal. i.e. it could be deleting
.DS_Stores when you delete a directory.