I have run into this before and I had to "squeeze" the flash filesystem to make the deletions dissappear. Take a look at the following link for more information
Router# squeeze filesystem:
Permanently deletes all files marked "deleted" on a Flash memory device.
Do you know if the flash has ever been completely erased. I can not confirm this but maybe for the squeeze command to show you will have first needed to erase the flash filesystem.
On Cisco 2600 and 3600 series routers,the entire flash file system needs to be erased once before the squeeze command can be used.