Hi, we are having the exact same issue, only this time it involves the recent versions.
After updating to WC 3.0, this notice popped up: “WooCommerce Data Update – We need to update your store’s database to the latest version. [Run the updater]”.
We ran the updater and the database was updated. But after a while like 5 minutes, the db version will go back to 2.6.14. The updater reappeared, we updated again. This cycle keeps repeating.
We tried all solutions suggested here but still the same. We have no other dev sites accessing the same database. We also tried deactivating all plugins (except WC) before updating WC db but still the same. We contacted our theme developer, they too can’t help.
