I investigated further, and found that one of the quarantined files had not been fixed, it still had a big chunk of heavily obfuscated code in it. I assumed it was malware and removed it, it seems to have fixed the problem. Now checking other quarantined files.
I still am not sure how the plugin reports that the site did not break, when in fact the homepage returned an internal server error.
After the fix it loads the wp-admin in that framed window, if the wp-admin loads tht means the WordPress bootstrap was not broken. Theme files are often infected and con sometime be broken when they are hacked (if the hack was done poorly), or when the hack is removed (if the removal was not complete and thorough).
Can you send me the threat that you had to remove yourself? If my plugin could have removed that whole threat when you ran the fix then this would not have happened.
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Two installations and two donations. Worth every penny. Eli's plugin found a ton of stuff Sucuri didn't find. Thank you, Eli, for building a great tool to help us keep our Wordpress sites secure! -- Gary Cope
Thank you! Just donated $50.00! You deserve it! -- Stewart
Just wanted to say how much easier your plugin has made to my life & management of my sites! Malware was constantly being injected into my WP sites so much so that Blue Host shut 2 sites down twice. I'd no sooner get them cleaned and I'd be infected again. The amount of money I paid for cleaning and patching was astronomical. I am not a web builder or coder and clearly I was taken advantage of. I found your plugin through a search, installed on sites, (very easy) and now I run scans on my own, clean what comes and have saved myself a small fortune. I have recommended your plugin to dozens of colleagues and I thank you so much for making this available to techies and non-techies (me)!> -- Lois