Why are my sous vide salmon fillets coming out raw in the center? My wife and I have tried a couple times to sous vide salmon fillets and they seem to keep coming out undercooked or raw in the center and I'm really not sure why.  I took pretty good notes on what we did tonight and I'm hoping someone can find the flaw in my strategy.

We purchased 1 lbs. of salmon fillet from Trader Joe's.  At home, we pulled it out of the refrigerator and cut the skin off of the salmon and cut it into two separate fillets.  I have a FoodSaver vacuum-sealer that I used to vacuum seal the two salmon fillets into a single bag.  The salmon fillets were vacuum-sealed in the same bag, but were not touching on another (they were about 3 inches apart).

I have an Anova Culinary sous vide that I used to get a water bath up to 126 degrees farenheit in a large All-Clad stainless steel pot.  Image of the sous vide setup below:



Once the sous vide was up to temperature at 126 degrees Farenheit, I dropped the vacuum-sealed-bag with the two salmon fillets into the pot and started a timer.  To be on the safe side, I left the salmon in the pot with the temperature at 126 Farenheit for one hour.

When I took the salmon out of the pot and opened the vacuum-sealed bag, it seemed like it was colder than I would expect.  Upon cutting into the salmon, I noticed that it was still raw in the center.

After I noticed the salmon was raw, I put a thermometer in the pot and verified that the temperature was 126 degrees Farenheit, so I think the sous vide is working properly.  From what I've read online, cooking for 1 hour at 126F should be more than enough.  Likewise I read that vacuum-sealing fish tends to end up with overcooked fish rather than undercooked so I didn't think that was the issue.

Where did I go wrong here?  Any suggestions would be greatly appreciated!  Thank you!
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.