Ok, I had same issue, will share with you how I solved this problem.
1. write to google antimalware and download free malwarebytes software.
2. check your computer for malware.
3. Erase all ftp and http (browser) history
4. Change passwords
5. Check all index, header files in all dirs to find iframes, also you will find some more files:
it's like when you erasing one iframe in index for example and trying them go to your site, you will see warning for different file>check that file and erase iframe (don't forget to look for broken code end, because these iframes are nasty, they like to break the code). DONT FORGET HTACCESS! - often shit comes from this
Troubleshoot:
let's say it didn't help...
then make again every step, but replace 5 step and make this proccess:
-make backup of your database (check google)
-make backup of your uploads
-delete everything
-install fresh site and put your database with uploads.
Write in google "how to delete iframes" and so on.
btw
I don't use ftp program anymore, I use firefox addon fireftp - its safier.
Don't forget permissions. NEVER 777 in themes and plugins, especially in those files which people can see.
Good luck mate.
I would write more, but my english is my wall.