I have found that replacing the files has worked on all but one of my sites :/ can’t explain why; did all the same things, have the same setups etc…
Thank you @iLabz just trying that now however it has come back negative saying there are no issues. Misread the post previously thought the suggestion was that Wordfence was causing the issue not a possible solution :/ Appreciated.
Also have just found that I have this problem. I’m with hostgator and all my sites are now showing the same error. I’m not using Wordfence however.
Haven’t tried the fixes found here; only just found it and off to try and fix now.
*** Edit ***
I have replaced the files:
/wp-includes/template-loader.php
/wp-includes/js/swfobject.js
…as suggested on one of my sites, however has not had the desired effect. I am still receiving the malware warning. Although looking at the history of these files I can see that they were both edited yesterday on all of my installations of WordPress (not by me).