I had some trouble with this so I thought I'd make a forum post so somebody may find this of use later on.
My problem was I was attempting to run "sake dev/buildcache flush=1" from my command line for later use as a nightly cron job (which I had to run as root). I was able to run "mysite.com/dev/buildcache?flush=1" in my browser with no problems. However, when I ran it using sake from the command line all of my resized images disappeared and left blank spots in the rendered code - I don't mean broken image links, the "img" tags were just mysteriously gone. Eventually I figured out this was because images that were rendered by SS in my assets folder were owned by Apache and I was running the script as root. Rather than relax permissions, the solution was to write a shell script that first chown'd everything in assets to root before running the sake command and then changing them back to Apache after the cache was built. Another related issue is that the cached files created by sake were owned by root and this made it impossible to update cached pages from the CMS. Again, to fix this I chown'd the cache files back to Apache after the completion of the script. With this script I now render 1,200+ pages (and growing) every night and come to the office with a freshly rendered site every morning.
I'd like to say static publisher is one of the best features of silverstripe and more than compensates for any of the overhead incurred from Sapphire and I heartily recommend everybody use it whenever possible. I have a number of custom page types and it is a snap to exclude the ones that can't be cached.
I hope this helps somebody, I know it was a tough nut to crack for me!