That is more likely an Object Cache problem, its your settings with W3 Total Cache. Turn off Object Cache or mess with the settings. Clear ALL caches.
Do you have another Object Cache such as APC?
You got to mess with the plugin, look at tutorials. Speed test it per your environment.
W3 Total Cache also has a Browser Cache area, some of the code added to .htaccess by the plugin might be the same or similar to “Speed Boost Cache Code”. Its a false positive.
Not sure what the overlap of code might do or if affect performance or causes header issues. You have to play with it and analyze it.