I think Brian should first confirm that the speed sensor is operating correctly and can pull it's 470 ohm pull-up to a low value - disconnected from other things. It it can't, there is a problem. If it can sink enough current through the 470 ohm to pull it "to ground", then it can also pull the port pin "to ground" and generate a LOW input. A modest series resistor is not an issue and can give some protection to the input. However, do not add capacitance to the MCU pin - that is the wrong way to go. Part of the problem may be the RC formed by the 100k and the MCU input capacitance blunts the step change of the sensor output; this would give an effect more pronounced at higher speeds, but would work fine at sufficently slow pulse rates.