I see people are complaining about Filezilla, I use this program 3 years, and I never had a problem with it. Maybe you downloaded a version that can steal your passwords (those kind of versions can exist as well as any other free open source programs can be modified, download only from secure sources) or maybe your computer got hacked and the attacker found out you have filezilla and looked for passwords or your server has a vulnerable script.
This wasn't caused by your FTP client. It was caused by an infected system which had been used to FTP. This could have been caused by a hijacked session or a key logger. I recommend you save important files and format your pc, and please use sftp (or ftps) from now on.