I am having a similar problem, though the cache isn't clearing itself at any particular time - it just frequently happens. I have over 20,000 posts/pages on the site, and I never see the cache count at larger than around 1,100. Some point after then it seems to reset, delete all my super cache files, and start again. I have garbage collection set to 0 and PRELOAD MODE activated. (says: "Supercache files will not be deleted regardless of age")
What gives? I want the files to cache all the time and never be refreshed unless I physically empty the cache myself. Thank you!