We just converted to XF1.3 from vBul 4. Everything is great - except the user upgrades aren't working. It looks like they're going through on the PayPal end, but there's nothing in the transaction log and no one is getting upgraded. They're not getting an error message, and don't understand why the upgrades aren't being applied.
Check the xf_user_upgrade_log table. Is there any record of the transaction? The record may contain a specific error message if there was a problem. If there is no record of the transaction then make sure the payment completed (in your paypal account). Also check these things:
1) Make sure your board URL is correct:
Admin CP -> Home -> Options -> Basic Board Information -> Board URL
2) Note that the paypal callbacks don't work if your forum is behind a htaccess login.
Or it's possible Paypal simply failed to send the callback. That happens sometimes in which case you can manually upgrade the user in the Admin CP.
These were just ones paid AFTER the migration. Nothing in the log table at all. But, I finally found the problem - our treasurer had IPN notifications turned off (I think there was some confusion on her end as to what that was). Solved! Now I just have to match up a ton of them by hand that have been paid for. . .