The Windchill FTA calculation is multiplying 10^-6 to the cut set events for model FR/MTBF but not for constant probability. How to prevent the 10^-6 adding upto the final value?

Are you saying that you do not want the failure rate entered in the events to have the failure rate multiplier of 10^-6 applied?  So if you entered a value of 10 for failure rate in a basic event, you would want that to represent 10 failures per hour and not 10 failures per million hours?

Go to "view" menu, and click "File Properties.."

Click small "+" button at the right side of "General", then you will see the Failure Rate Multiplier.

If it is set as 100000, you can change it to 1. 

Hope this is what you asked.