Yes, we are using W3-Total-Cache, as we are a busy site. Every hit that skips the cache is expensive, primarily because our sidebar is extremely cpu/database intensive.
And yes, I was mistaken, the polling frequency is a global setting. It was whether or not live discussion was enabled which was post by post (the _spectacula_threaded_comments_live, in wp_post_meta), as we were trying to disable the live discussions and we couldnt get them to stop.
I haven't put any coding time into WP plugins, as I manage mostly drupal sites, but is there really no way to just get the modified comments without going through the entire plugin process? no segmentation whatsoever?