Last night, several of my WordPress sites were compromised and I had to clean up the index.php files. Got rid of the script and all sites, except for three, are working correctly. Three of them, I cannot leave the page (by clicking X to close the window, nor can I type in a new URL in the address bar). The only way I can leave the page is to do a Ctrl-Alt-Del, open Task Manager, and close that way. Incidentally, those three 'home' pages are all left centered now, whereas they should be centered. All other pages within the site are OK. I think something has happened to their index.html files as well.
My sites are hosted through GoDaddy. They have confirmed there appears to be no malware or harmful script.
Can someone tell me what to look for?