James,
my take on it: If Godaddy already times out with a 500 error on a single non-cached page load, then imagine what it will do if it has to (pre)load 232 pages every 30 or 60 minutes... It will take a long time. So my bet is that the preloading cycle does not finish regularly, thus you always have a lot of uncached pages.
I am not sure but think that when preloading, Supercache first deletes the previously loaded pages and then the preloading starts. So if preloading is that slow, there is a good chance you will hit a non-cached page.
So the task to do is to watch the progress of the preloading. If you see indeed the preloading going very slow, not finishing in its cycle, then that is the problem you saw to start with "Why am i seeing so many noncached pages"...
On Godaddy, the only thing that could help you a bit, is to go to gridhosting (does not cost you anything, and is done for free, automatic and conversion is done pretty fast). Grid shared hosting is emmm.. less unreliable.
Since I left Godaddy for Hostgator, my life took a turn for the better. (I went pretty far, and went for VPS hosting, so I could control the whole server setup... Night and day difference.)
PS: I still have several test servers on GoDaddy I use to design new blogs. On several of them, with 200 posts content, I have caching running to test things out. I often get an automated email from supercache that the preloading stalled. So there you go.
Peter