foisya on "[Plugin: Wordfence Security] cannot perform scan"

I have installed Wordfence on a few sites and it has always worked well.
However I'm having a problem running it on a particular site and the only difference is that Wordpress is installed in a subdirectory and not at the root of the homepage.
I've read a few forums and this had been reported as an issue in the past and was fixed in an earlier Wordfence update. However it doesn't seem to be working for me.
I click on scan and it displays Requesting a New Scan and it turns for a few seconds the does nothing. Nothing appears in the Detailed Activity.
I know for a fact that my site contains a Trojan and would love to be able to fix it with Wordfence.

http://wordpress.org/plugins/wordfence/