You shouldn't faction change a character that still needs to logon after a realm transfer. You can see that by it's name. Logon to it, select the name, make sure you don't have any new mail, then faction change.
10/04/2012 02:36 PMPosted by GöküCan anyone explain this:
Yes, you have the original character that you are faction changing as well as the new version awaiting transformation.
The process itself is still pending because it looks to be awaiting payment confirmation. Make sure that you have created a Billing Profile for the method of payment you are using.
Ishammy, I'd recommend the same thing. You can also visit the Race change History/Status page to see if you need to update anything, you may also cancel the transaction there.
Race Change History/Status: https://us.battle.net/account/management/wow/services/prc-history.html