Oh, are you saying that you have set up "Rate 2" in the Pay Rates section on the employee screen?  If so, I've never known the Rate 2 and Rate 3 fields to be anything other than for reference.  I do not know if or how the system would automatically pick those up for anything.  Typically the system will calculate OT based off of Std/Rate Salary field.  Is your OT not paid at 1.5 time the normal hourly rate?  If not, maybe if you change the OT factor to whatever you pay - perhaps if it's double time for instance - set it to "2". 

Good luck!