Hi Hiarlen thanks for responding! If you are referring to the domain mapping setting - I'm not using it. We use the Sitewide Tags solution to create the primary blog.
I did find the problem late last night forgot to update this thread. There's a checkbox on the Advanced screen for Extra Homepage checks. I found a comment deep inside a forum post where Donncha suggested that sometimes this could cause Homepage caching to stop. Well, that was the ticket - it stopped homepage caching on some (but apparently not all) subsites for us.
I also think in doing all this that I found a solution for the occasional post showing up as a homepage, and it's related to the complexity of one's .htaccess file. If you have significant rewrite conditions outside of the standard WP MU .htaccess entries, it's impossible to tell from the instructions where the WP Super Cache .htaccess modifications should reside.
I've tried the WPSC entries both BEFORE the rewrites and AFTER. Our current config has WPSC BEFORE the rewrites and the site is a bit quirkier than when they were AFTER the rewrites -- but before the standard WP MU entries.
Overall the plugin works but there are definitely quirks and bugs. My favorite is when you try and install supplemental caching (like xcache or APC) and it either (1) scrambles the database until removed, or (2) interrupts the GC routine and causes actual WP-CRON 'code' to appear on all the sites and dashboards, even to logged out viewers, as the WP-CRON job gets fouled and the only way to fix it is to ssh into the server and manually delete the WPSC directory. Had that happen twice so far.