Filezilla alternative - iframe hacks

Hello

I keep getting my sites hacked via iframe injections. I have read many solutions from digitalpoint and filezilla forums (filezilla is the program I am using) but they do not work - I save the passwords on my machine via the filezilla xml file - my passwords are like:

"F"£<FO2k023F"£@F"£@F"£F@£"F

They still get hacked. I need a program that does FTP that you can saved passwords on your machine securely. Anyone know a good one? Free preferably?