I've been using this plugin for almost a year and it's been great. I've never had any complaints with it.
But, a few days back my site was taken down by the hosts, because, they said, it was hogging about 2/3rds of the server's resources. After looking into it, they said "the page /wp-cron.php?doing_wp_cron is being hit sometimes as many as 4 times per second."
I also noticed that my admin became unbearably slow. It's always been laggy with W3 total cache active, but it was taking more than a minute for any page to load.
Anyways, I don't know anything about crons, so all I could think to so is deactivate my plugins. W3 total cache was the second one I tried--and as soon as I did, my site started moving as fast as a fresh install. I got in touch with the hosts right away, and a little while later they told me that the problem appears to be solved.
I know you have your hands full here, but you might want to look into this. I mean, if W3 total cache is going to bring down servers, than it kinda defeats the purpose of having it.