I think this bug has been fixed a couple of years ago, but it seems it has surfaced once again: when copying a database from one host to another (in my case: from our development server to our test server), all is copied perfectly… except for the autoincrement attribute on the primary key. Somehow this is removed in the process. I am copying both the structure and the data.
I found a workaround for now by making an SQL dump (“Backup database as SQL dump”) of the whole database and importing it again on the other server, but I think that is about the same the “copy database to a different host/database” option should do.
I am using SQLYog Ultimate 64 v12.15 (64 bit). Both servers are using an SSH tunnel. The database I am trying to copy is a Typo3 CMS 6.3 installation. If you need any more information, please let me know.