Taking a sample for OG question

I feel silly asking this because with 7 years of homebrewing experience I'm hardly a beginner. The thing is that I've never worried much about the alcohol content of the beers I brew. I aimed for a flavor and let the rest take care of itself. Recently I bought a wine thief (beer thief in this case) and decided to put the hydrometer to use finally. The first batch was a Summer Saison mini-mash. I did the boil and then added water to bring the volume up to 5.5 gallons. As normal, there was a lot of coagulated protein in the wort but I didn't want to let the wort sit uncovered so I used the thief to draw a sample, protein and all. The reading was higher than the recipe said it should be. Two days later I did another mini-mash, Texas Blonde. This time I let the wort sit until most of the protein had settled before taking the sample. The reading was lower than I expected according to the recipe. In both cases I adjusted for the temperature of the wort. What I'm wanting to know is, when is the correct time to draw the sample? Does the presence of the protein make a difference? Both batches are currently in the secondary fermenters and it will be some days more before I can draw a FG sample and keg. After not paying much attention to alcohol content for so many years, my curiousity is killing me.

Thanks,
John

I don't think I've ever had enough protein to figure it would make a difference. My protein usually all falls out with the cold break, then I strain going into the fermentor. I take a reading at this time and adjust for temps. It sounds to me like you're having an issue with the added water not being completely mixed.

That could be. I don't strain the wort as it goes into the primary so there were clumps of protein and Whirl Floc present the first time around. The second time I let things settle and was wondering if the heavier sugars had settled as well. Oh well, I'll have an answer in a few days when the beer is ready to keg and I can take the second reading.

Thanks,
John