Why are my sous vide salmon fillets coming out raw in the center?
Your set-up is fine. You'll probably eventually want to trade in the stock-pot for something like this:



But there is no reason that the set-up you have shouldn't make great salmon. I have exactly that set-up (including the stock-pot for now, but the square polypolycarbonate container is on order). 

125F for one hour is pretty close to bare minimum time and temperature for salmon fillet. I like it that way, but it appears that you have a different expectation than I do. I base that guideline on the recipe from Modernist Cooking Made Easy: Sous Vide: The Authoritative Guide to Low Temperature Precision Cooking and having just enjoyed salmon done at 122F for 1 hour.

First, double check your water temperature just to be sure. If you have a sous-vide circulator and a vacuum sealer, I don't want to hear that you don't have a digital, instant read thermometer. Double check that your Anova circulator is producing the temperature for which it is set. If the temperature is how you've set it, that means that you don't like your salmon that rare. Simple as that.

140F for 1.5 hours is pretty much the upper limit for a typical salmon filet to not be overcooked. That would be overcooked for me, but I have a preference for rare. 

Assuming that your circulator isn't defective, you will almost certainly like salmon somewhere on that spectrum. Exactly where you like it best, only you can say.