I have the Domain Mapping plug in set up so all my multisite blogs can have their own URLs.
I recently set up a new site and did have wp super cache working really well but now something seems to be out of whack.
I noticed the other day that while the internal pages (e.g. blogurl.com/internal-page-title) were loading quickly that the home page was noticeably slower.
A quick check of the source revealed that there was no "dynamic page generated... etc" message on the home page (but all internal pages are being cached).
Testing the cache in the dashboard gives me "two timestamps don't match" but the test uses the home page URL for the sub domain of the site (e.g. blogsub.multisitemainurl.com instead of blogurl.com).
So it seems that for the homepage at least wp super cache isn't looking at the right page.
I've tried deleting all the relevant cache files in the wp-content/cache folder but the entry for blogsub.multisitemainurl.com keeps reappearing in the cache/blogs folder.
Debugging doesn't seem to be giving any useful information either: there is a debug file but it doesn't seem to update when I click through the site. If I delete the debug file in the hope a new one gets written the old one comes back!
I've tried wiping out the wp-content/cache folder to force writing new data but there doesn't seem to be any change: both versions of the site domain crop up in wp-content/cache/blogs (blogsub.multisitemainurl.com and blogurl.com). The old debug file also reappears.