440kHz and 540kHz.
1/440000 = 2.72uS too fast for pulse in.
Options:
Run the signals thru a low pass filter, get a DC-ish level out and read in via ADC.
http://sim.okawa-denshi.jp/en/CRlowkeisan.htm
Set for say 490kHz; 540KHz will have lower output level than 440 KHz.
Use a counter input, count the number of pulses that occur in 1mS.
440 & 540. Both will wrap around on an 8-bit counter - so ~185 & ~285 get returned instead.