Until now, I had been unaware of the earliest usage shown below, and I had always understood the boxing reference to be the origin. Live and Learn!

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To be “thrown for a loop” or “knocked for a loop” refers to being bewildered, dazzled, disoriented and shocked by some event (“AT&T and T-Mobile were thrown for a loop last week when the Department of Justice sued to block AT&T’s planned acquisition of T-Mobile,” CNET, 9/5/11). The phrase first appeared in print in the 1920s, and comes from what the Oxford English Dictionary terms “a centrifugal railway,” but which is, no doubt, better known as a “roller coaster.” The “loop” on roller coaster runs is the point where the coaster arcs upward through a complete circle, leaving passengers upside down at its apex. The term was initially used in the literal roller coaster sense and then to describe aerobatic maneuvers by pilots “looping the loop,” and finally in boxing to mean a powerful punch that downed an opponent, before acquiring its modern “OMG!” usage.

http://www.word-detective.com/2012/04/knock-for-a-loop-knock...

I've also heard it as "knock me for a loop", and I think it calls back to "feeling loopy" as a sort of "dizzy", so to throw/knock someone for a loop is to metaphorically hit them so hard as to make them dizzy or disoriented.

It doesn't refer to anything that I am aware, it simply has the connotation of "looping" back, much like "doing a double take".