I have the same problem, on a "network install".
I have the last version of WP and WP SuperCache.
When I set PRELOAD with a delay (60 minutes), I see "next preload in 59m40s". If I ask for a PRELOAD with the buton, the preload is effective, but after a delay (auto preload delay ?), all preloaded pages a deleted, and there is no new auto preload.
there is few topics about the same problem on this forum.
A bug?
thanks for your help.