I have used Core ftp Lite twice, but I am wondering where I find the command to force lowercase on transfer, as some of my files have UPPER CASE characters, and they need to be lowercase on my host's server.
Under the advanced settings of your site profile (in the Site Manager) there is an option under "Transfers" that you will need to check - "Uppercase all destination filenames".
The next time you connect, all filenames should be lowercased.