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 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.