Yes, it sounds like a virus on the host server, probably from an insecure script not necessarily from your site.
Check your hosts server is up to date and virus free.
Then change all your ftp and host login password etc and also run a full virus scan on your local computer. It may be you have a virus on your own computer that attaches itself while you upload via ftp.
The virus/script may be browser selective (attaches to a vulnerability in certain browsers) which is why maybe all will not see it.
If you google "site hacked with iframe" you will get a load of suggestions as to what might be the cause.
Good luck these things are a nightmare.