If you are sure you got water out of the filter drain, then you have water in the fuel.
In the sample in the bottle there does not appear to be any water - therefore when you pumped some out of the tank, the end of the hose was not below the water/fuel interface and you just got fuel.
Push you pipe in until you feel it hit bottom, then remove some "fuel" and see if that settles out.
You may only have a couple of inches of water - I had over 200 litres of water in my tank.
When you say you refiled your tank from empty - do you really mean the tank was empty, or there was no fuel ciming from the tank to the filter - the fuel to filter pick up pipe (inside the tank) is normally several inches off the bottom of the tank so as to avoid picking up muck, rust, rubbish and water.
If you drained the tank until no fuel got to the filter, you probably have left 'inches' of water in the bottom of the tank.
Ideally you should (properly) de-water your tank annually.