you can solve this problem by writing a seperate script(not a batch file) i.e a simple text file which contains your username/pwd and any other automated steps and referencing this script from your batch file.
here is an example i used to FTP files to another server
ftps -c:600 -t:600 -s:PutNewFiles.txt
del *.txt
del *.blk
del *.mpg
In the above example, "PutNewFiles.txt" is a txt file that has the following information
open 192.168.2.xxx
username
password
bin
ls
mput st*.zip
when the batch file is run and the ftp starts, since the batch file gives control to the ftp program, the script is used to carry out ftp functions and control is passed back to the batch file once the ftp is complete