“Being unable to run” is definitely “some other impairment” and flawless stride thus ignores it. So a scout is never prevented from running (or otherwise moving exactly how she would like to and otherwise could) by the features of a square. Darkness isn’t a feature of the square, and yes the scout still needs line-of-sight, but “terrain” offers no impediment. (More on that “terrain” in a bit.)
This is a basic function of the rules, which are known as “exception-based.” There are general rules for things (no running through difficult terrain), and then classes, items, feats, spells, and so on grant “exceptions,” which are basically little, specific forms of sanctioned “cheating,” breaking the general rules (in this case, the scout’s ability to move unhindered through terrain, which allows her to break the rule about not running through difficult terrain among other things).
That said, there are still some sticking points worth describing.
First, what is “normal speed”? Generally speaking, the rules refer to “how things would otherwise be if the exception we’re talking about wasn’t in play” as “normal.” This is really awkward and occasionally confusing, for example with polymorphing where one’s “normal” form is the form you had prior to casting the polymorph effect—not necessarily some “base” or “natural” form. But nonetheless, the rules are pretty consistent about this definition, and it certainly makes the most sense here. Clearly, the flawless stride ability should not be preventing the scout from benefiting from some movement speed bonus and locking her to some “normal speed.”
Secondly, what actually is “terrain”? The DMG describes a number of environmental features as “terrain” and it is conceivable that the flawless stride refers to only these things (the parenthetical examples in flawless stride, certainly, are all these sorts of terrain). However, personally I would certainly also include any sort of “difficult terrain” as a type of terrain that flawless stride allows you to ignore, even if not part of any of the DMG’s “terrains.”
Actually, myself, I would allow the scout to ignore any amount of undergrowth, brambles, sticky goo, and so on, as long as it wasn’t magical. And that can even include spell effects! Spellcasters are awfully fond of their instantaneous creation spells that operate just fine in an antimagic field since those effects are “not magic,” so I would certainly be inclined to force them to put their money where their mouth is and consistently have it be non-magical—including allowing a scout to ignore it.