VERIFIED SOLUTION i
This error was because there are many different ways for FTP authentification to occur, and Manifest Uploader does not support all of them at this time.
For the IBMi customer who received this error, it was suggested that instead of having Manifest Uploader try to connect to the IBMi to get the files, that he have MailStream Plus running on the IBMi machine write the Mail.dat files onto the IBMi's IFS (Integrated file system) drive. And then Manifest Uploader running on Windows can read the files from the IFS drive.
UPDATED: August 28, 2017