The chip is programmable for tire size, which works out to revolutions per mile, and pulses per mile. Probably just a bit of math involved, entered into a couple of fields.
The tach should not be programmable in the tune. RPMs are RPMs.
Is it off by a factor of "twice what it should be reading"? Your DIS might be set up as a "wasted spark" system. (I think they all are?) If so, it's possibly reading a pulse on the exhaust stroke, too. Depends upon where the tach gets its feed. If it's just randomly off (which mine was) it's not a terribly ugly fix. Cut one trace on the tach board. Solder in two wires to the board, and a 1 Megohm variable resistor to the other end of the wires. The capacitor in your tach has probably changed value. Will probably continue to change.