I'm still trying to find the exact cause of the problem, but if converting from phpBB 2 to phpBB 3 with MySQLi enabled (in the converter options), only parts of the old board will be converted. Usually, it takes me up to 8 hours to fully convert my board properly. However, with MySQLi enabled, it took an unsually short amount of time (1.5 hours). After improper conversion, all seemed well until I tried to view the board. There were no forums though the forums database was intact. Only half of the users were converted.
I re-did the conversion with MySQLi enabled and the same thing occurred. I finally re-did it without MySQLi and it converted everything properly.