Join Date: Jul 2005
Location: Boulder County, CO
Bikes: '79 Gios, '80 Masi, '06 Felt, early '60s Frejus
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3mm of engagement is not a lot, but on the other hand I've seen the damage caused by not fully engaged splines, and it's not pretty. In this case it was an isis right crank that worked loose, causing strippage of about half the depth of the splines. There was enough spline left that I could reattach the crank after aligning what was left of the splines to the spindle, so the guy could ride home very carefully.
More important, though, is the 3mm less engagement by the left crank end bolt, possible trouble caused by the pinch bolts clamping down on it in its partially engaged state, and how that might lead to a loose crank arm and stripped splines.
The whole thing smells fishy to me. I'd try for a refund and get a BB sized correctly for Shimano.