Data on the slave becomes inconsistent after couple of days

We are planning on upgrading our production MySQL server from MySQL 5.0.77 to Percona 5.6.19-67.0. Since our downtime window is small, we setup a slave of the production master on a new host and upgraded it from MySQL 5.0.77 to MySQL 5.1 to MySQL 5.5 and finally to Percona 5.6. Here are the steps we ran:

  1. On master, we ran innobackupex to generate the backup
  2. Prepared the backup with innobackupex --apply-log option
  3. rsync’d the backup folder to the new host
  4. changed the name and ownership of the folder on the new host
  5. installed mysql 5.0.77 using rpm’s
  6. started the mysql server after pointing the datadir variable to the folder which was copied from the master
  7. ran the change master and initialized the slave
  8. started the slave and allowed it to sync with the master
  9. once the slave was in sync, shutdown the slave
  10. uninstalled 5.0.77 and installed 5.1 using rpm’s
  11. started the mysql server
  12. ran mysql_upgrade
  13. fixed all the tables which were reported by the upgrade program
  14. repeated the steps 10,11, 12, 13 for upgrading from 5.1 to 5.5
  15. uninstalled mysql 5.5 and installed Percona 5.6
  16. started the mysql server
  17. ran mysql_upgrade
  18. fixed all the tables which were reported by the upgrade program
  19. started the slave

Upgrade went smoothly. After couple of days, data on the slave has become inconsistent with the master. In one of the tables we found that rows present in the master are missing on the slave and slave has some rows which are not present in the master. How is this possible? Did we do anything in the upgrade process which should not have been done? Has anyone else faced similar issue? Please let us know what you did to resolve this issue, if you faced it.

Thanking you all in anticipation,