An undeletable file huh? Use "site swho" and see if there isn't some connection stuck trying to upload the file or something. I've seen zipscripts (especially the .exe variety) get stuck before and that would leave the file with an open handle or two. It also occurs to me that the internal ioFTPD-only read/write lock on the file only applies to the files contents and it could probably be "deleted" but exactly when depends on how windows handles open files being deleted. Just for kicks try to upload the file again while it's in this weird state and carefully record the error message.
If you were using "Encryption_Protocol = TLS" then you do limit yourself to a pure TLS handshake for logging in and data transfers. There's even a warning that if you do set this you'll probably have to tweak some other settings. I suggest you leave it commented out
