Not clear where the problem is from your description.
What IBM i operating system are you using?
Are you piping the IFS script file into an OS/400 FTP command, or are you running ftp within PASE/QSHELL (or something else altogether)?
Are the user profile and password embedded in the script?
Are you retrieving them from environment variables within the script?
Are you using values from the users home directory?
Are you trying to pass them as parameters from the IBM i environment?
FWIW, I've been using Scott Klement's FTPAPI service program on IBM i5/OS v5r4 when I need to ftp. Superior error handling versus batch scripting. No problem connecting with mixed case usernames or passwords,