"R1 reaches 2nd just right before the ball arrives, hitting the F6"
The way your have described this would be identical to F3 stretching to the left infield awaiting a throw from F6 - and the B-R cuts inside the base (forget the issue of double 1B) and hits the fielder - causing her to be out of position when the ball reaches 1B.
If that is true, than it is obviously interference. But the umpires confered and they saw obstruction. So they obviously saw something different than you did. From here I can't guess what it should have been.
WMB
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