> Does deleting a file with a dot at the start of the name work from the command line ftp client?

yes it does from ftp-0.17-70.fc24.x86_64
Windows ftp client gets its butt kicked out as it doesn't support passive mode

>What commands does the command line client send?

delete filename

>Does it work if your program sends the same commands?

Can't test as their Internet is down. I will soon try "quot"

I sincerely appreciate all you guys help

When the customer's Internet comes back up, I have a test script I will run at it and report over to the bug I created on this at
https://rt.cpan.org/Public/Bug/Display.html?id=120140
The bug contain versions etc.