How many websites do you have in your reseller account?
Any one of your website might have malware script, after cleaning also it spreading it to other websites.
You might need to find that loop hole script and delete them, finally you have to change all passwords.
I don't have much experience in Web Security, if your reseller account disk space is not much bigger, then make a complete backup, download it locally.
Scan it with your virus scanner, it might inform you the malware spreading script, note down the filepath and delete it on your server.
That's my suggestion.