[Plugin: WP Super Cache] Preload on a Multi-User site

I tried enabling preloading on some blogs in a multi-user setup, but I’m not getting consistent results.

So I’ve done as follows:
1) Turned off Garbage Collection (Cache Timeout == 0 seconds)
2) Turned on Preload Mode (every 1440 minutes)
3) Clicked “Preload Cache Now” when in the main site’s Dashboard
3) Clicked “Preload Cache Now” when in another (sub)site’s Dashboard

Mostly this works (an excellent plugin, by the way) but I’ve had some issues:
1) Cache randomly clears. Not sure if this is right after I do a “Preload Cache Now”, but I’ve had all cache clear without any obvious reason (I have “Clear all cache files when a post or page is published or updated” unchecked).
2) Sub-site’s home page does not get cached (but the rest of the pages in the sub-site do).

Is there something I’m doing wrong, or some option I have enabled/disabled that needs to be toggled?

I was also curious about how this works on a Multi-User site in general:
I notice that once “Preload Mode” is enabled, it seems to be enabled on all sub-sites… or at least the checkbox is checked. It does not seem to be Preloading every sub-site, however. How come? Is there a way to actually enable Preload Mode for all sub-sites? Or even run a “Preload Cache Now” for all sub-sites?

Thanks for your time. Any answers would be most appreciated.

http://wordpress.org/extend/plugins/wp-super-cache/