poping sound from brake btsi cover when I brake
 

2008 ford escape, 39000 miles. The car would not shift with the shifter andle. Opened manual and poped off the btsi cover and pushed the brake-shift interlock as the book said to do. Car shifted and than the wrench symbol came on the dashboard along with the check engine light. Mechanic checked the code and it said transmission. Car drives and shifts fine but now when I brake there is a poping sound when I push the brake padal coming from the consloe btsi. Just for a split second. All the lights are working. Dash lights check engine and wrench light are still on. Any ideas?
Thanks