Usually a 3:1 flush is all you need to correct problems with ph and nute issues. (3 gallons of ph'd water, for every one gallon of soil volume)

If more than one flush is needed, let pot sit till soil dries out a bit. Otherwise, root rot from overwatering is a strong possibility.

My guess is that Stinky is right. (is she ever wrong, lol..?) Likely you are seeing small, dark particulate matter that will settle-out after a few minutes. Does it really matter with your liquid ph tester, tho? If there is any color at all to the run-off water, won't it skew the color-coded test results? My aquarium water ph test kit was unusable for run-off, for just that reason.

Milwaukee ph test pen...$60.00.

Stinky:
We often suffer from deja vu. Problem is...newbies suffer from vu ja-de. (that feeling you've never been there before)