[Plugin: W3 Total Cache] WordPress in subdirectory problem with cache

I have WordPress installed in a subdirectory and redirect my website’s homepage to the subdirectory with a 301 redirect to prevent duplicate content. That works O.K. until I install W3 Total cache. In that case the redirect seems to be bypassed which generates duplicate content for my homepage content and the subdirectory content.

Any solution would be highly appreciates because W3 Total Cache seems to be the right solution to speed up my site.