The "import from Opera" wizard where you choose an accounts.ini file is a little simplistic. It just imports the account settings to set the accounts up and then imports the database stuff and messages. This means that if there's something messed up with the database, you're going to get that corruption again when you import from it.
As for why things appear at first and then disappear, I'd guess that Opera ends up hitting something invalid causing them to disappear in the same way they're not there in the original mail folder.