Few things are time critical with sous vide, so on the whole the timer is superfluous. Fish is one of those few things.
You say your salmon is mushy.... now, this could be that you're are not used to the texture produced at the temperature you've used to cook it. You might need to cook at a higher temperature to get more setting of the proteins producing a more traditional texture that you prefer.
It might be that you've cooked it too long for the thickness of the fish. Thickness is a variable that is difficult for recipe writers to make allowances for.
Because fish can be time critical, I would definitely make sure you don't put it in the water bath before temperature is reached. The until shouldn't take much time to recover from the slight temp dip of adding your product, so it is ok to start the time count once your fish is added to the bath.