All of my email accounts seem to be working just fine, and in the main inboxes, emails from VIPs are marked with stars next to the senders' names as usual. The issue is that all of the VIP-specific mailboxes show up as having 0 messages, even the big "VIPs" one (the one that contains mail from all VIPs). Un-starring and re-starring the contacts doesn't fix anything. I can still search for the messages by the contact and find everything, it just doesn't show up in their VIP mailbox in the sidebar.
Another helpful observation: Turns out VIPs work fine on my two rarely-used email accounts (Verizon and iCloud) that aren't Gmail. I knew OS X didn't like Gmail, but I've never seen this before.
This has been going on for as long as I can remember on El Cap, from the first public beta all the way to the newly-released 10.11.1 public beta. How do I fix it?