Hi,
Hmm, OK, so at the lowest frequency, how wide is the pulse comming from the "seed slot sensor"? Ie, what's the dutycycle ratio and are the slots equally wide on a 12 slot disc as they are on a 160 slot disc? (I suspect they aren't...)

I mean, you're obviously not going to measure frequency since the gate time would have to be long to get the resolution. You're going to have to measure pulsewidth and convert that to frequency, which I suspect is what intended anyway, but if the seed slots in the discs are different you're going to have to either cater for that or measure both the slot and the "space". Ie a full period.

I'm not sure why you're worried about the leading edges not being aligned. I don't see the problem.

Another aproach could be to use a timer and the interrupt on change feature. When ever an input changes state grab the timer value and calculate the difference from last state change for the pin in question.

Just thinking out loud....

/Henrik.