Are you running aftermarket rotors? A local guy I know is running OEM style Brembo rotors and had to take out the anti-vibration shims for the first 10K miles when he changed his pads.
If the one that did slide on felt tight then you should leave it on in that state either.. it may glaze.
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Okay... wait, i understand now... there IS space in between the pads for the rotor, but when mounted the outer face doesn't clear the outer pad, but there's ample room between inner face and pad?
Pull the rotor and clean the hub bore with sandpaper and the same for the hub.
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Another way of fully seating the rotor is to just leave the caliper off and mount the rims, they'll press it back on the rest of the way. I prefer cleaning the bore and hub though as it ensures easier removal the next time. Even with the cleaning you may have to still mount the rim, but I usually don't. HTH