If there are no entries in the transaction log, PayPal isn't calling back to your server (or it isn't reaching you). Have you changed anything such as your installation URL? If so, are you redirecting requests from the old location to the new?
If not, it seems likely that IPNs would have been disabled in your PayPal account. Please log in and check that it is enabled. (Unfortunately, I'm not totally sure where they stuck it in the new UI; I believe it used to be under selling preferences.) If it's not, re-enable it, but it's unlikely to resolve the issue for previous users. You may need to use the "manually upgrade user" option (from the user upgrade list) to trigger the upgrades for the missed payments.