I had the same issue in windows. In addition to copying the ib* files and the mysql directory under thd data directory, I also had to match the my.ini file.
The my.ini file from my previous installation did not have the following line:
innodb-page-size=65536
But my new installation did. Possibly because I did not have that option in the older installer. I removed this and restarted the service and the tables worked as expected. In short, make sure that the new my.ini file is a replica of the old one, with the only exception being the datadir, the plugin-dir and the port#, depending upon your new installation.