I never had any trouble inflating mine using the Shimano valve, with this caveat: - I had to carefully seat the tire beads around the valve area. Make sure the beads rest right down on the rim and are not being held up slightly because of the rubber valve base. In fact, I find this important on all my tubeless wheels, not just the Shimano.
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2010 Cannondale CAAD9-4, 1978 Jack Taylor "Tour of Britain" #7338, 1969 Jack Taylor Ladies "Tourist" #5935 (wife's), 2010 Specialized Dolce (wife's)