Well, just to commiserate, not that long ago I migrated an application from a CentOS 5 server to a CentOS 6 server. The CentOS 6 server was faster hardware by every measure, and you could feel it.
But my MySQL table data load times (insert statements through Perl DBI) nearly tripled. Spent too much time searching for a cause and solution without success. Despite the stupid slow load times, the application itself 'did' run faster overall for day to day use (or at least fast enough) and I left it at that. Probably an averaging out of code execution vs query execution
There 'is' something wrong with the Perl/DBI/MySQL performance in CentOS 6. I continue with the assumption that somebody will eventually find the reason and a patch will fix it. In the mean time I accept that the table loads will be slower (a not too often initialization step) and the daily operation is fast enough.