The amplifier output is how I measured it.Where did you measure it? At the sensor itself or at the amplifier output?
Unless you have changed the transmission (and hence reluctor wheel tooth count), or the TCU, the amplifier output frequency should be what the TCU is expecting, since the amplifier output frequency equals the sensor signal frequency. The only other way in which the measured frequency could be half what the TCU expects is if the meter you used doesn't respond accurately to non-sinusoidal signals or the circuit is clipping off negative peaks and the meter sees only the positive peaks. Perhaps your TCU needs dual-polarity peaks to recognise the sensor presence?