Comments broken - can't seem to read or write comments tables

Hi, we've got a strange problem we've been unable to figure out: On a WP Multisite, one single sub-site has all comments are missing, and it 404's when we try to add a comment on a post. I've looked at the database via phpMyAdmin and the comments are all still there in the database. But you click the comments section in the admin, and nothing shows up there. Try to add a comment from the admin and it doesn't work from there either.

It's weird, it's like the comments & comments meta tables are still there, but WP can't read from or write to them. As far as I know it can read/write just fine on any other tables. I've tried repairing all tables and optimizing them from phpMyAdmin, but it seems to have no affect. We also tried a comment on another sub-site, that worked fine. We tried reverting to the TwentyTwelve theme and it still wouldn't work, so we assume it's not the theme. We also tried disabling all plugins, and that didn't help either. Any ideas? Has anyone seen this before?

Our hosting people said they've seen it before and never figured out a fix. The only thing they knew of was the work around of using a tool to export, then rebuild/re-deploy the entire site, or use something like BackupBuddy to export the sub-site then re-import it. I'm hoping someone has some other ideas. There must be a cause and solution.