The chronograph was designed to test velocity of rifle bullets, a solid mass. They are "ok" for testing a shot pellet load but the density of the mass does affect the readings. At what distance did you shoot the test patterns? Of course the full choke would emit a slightly denser mass than the modified choke. The chronograph reads the first recognizable "mass" it "sees" to trigger the reading, therefore the tighter grouping may read as 'faster'. (fewer pellets spreading ahead of the mass)
Also, statistically, it would be best to perform 3 groups of 5 shots to get an average. Were the shells factory or handloads? It is not uncommon for factory loads to vary +/-10% for field loads. If handloaded, due to the slower process, shells tend to be more equal. Not to worry about factory loads; you can't physically tell the difference and the velocity difference on a target or a game bird makes no material difference, at all.
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