Is it in a mining area or limestone area?
No. Well, I dunno, you'd have to ask Fox. But it doesn't have to be either.
Freestone brookie streams do this commonly, just not for long distances. i.e. the "drain" is only a short distance from the re-emergent "spring" in freestoners, rarely more than 100 feet, and typically much less. In limestoners, it can be miles.
You notice it a lot on the smaller, higher gradient streams when it's low and clear. Many times the stream will be dry or nearly dry in the riffles, but there's still plenty of current in the pools, which obviously makes you think. I think many underestimate how much of the flow of some of these streams is underground, or at least under rock/rubble instead of over it. But it only happens on the steeper parts, it pretty much ends when you get down to bedrock (and usually the fishing gets worse, too).
And, Chaz, I know we share familiarity with a few streams that do this.