[murph16]

Wow, seems almost every thread the past few days directly relates to stuff I'm doing.
I spent three hours cleaning up my HD yesterday, and noticed the same problem. I don't know how it happens, but simply closing Pro Tools and opening it back up got the Delete option to come back. Strange.
Meanwhile, I discovered that even after getting the files "deleted", sometimes the files still showed up in an "audio files" folder somewhere else. I went to My Computer, clicked on the drive, found this mysterious Audio files" folder, and then manually previewed each one in winamp, one at a time and deleted them again. This time they were gone for good. Finally.
Apparently, PT was making copies of some files and saving them in a separate folder.
After I was done, I deleted the empty folder and organized my sessions.
When all was said and done, I went from 36% available space to 56% available space, but it took three steps of deleting in some cases.
Time consuming, but worth it.
Now that I've deleted these extra folders, we'll see if it stays more organized.