Too much flow could be an issue, though if that were the case, I doubt the brain would open up right now. It'd probably want to stay closed to prevent anymore tissue from being damaged from water flow.
Is it possible it was handled a little roughly upon introduction in the tank?
Make sure the brain is away from any other coral. Favia do have sweeper tentacles (can be long ones too), so that may be stinging the brain also. Check at night time with a flashlight.
When I use two part, I dump in the alkalinity, immediately followed by the calcium. I don't wait 15 minutes, nor do I think it is entirely necessary to do so. You won't have any issues with "burning" your corals with the two part unless you dose the two part right onto a coral with insufficient flow. You're dosing into the overflow, so shouldn't be an issue. If you were having pH problems, I'm sure you'd be able to see other problems in your tank, not just in the brain. What is your calcium and alkalinity at? HTH