UART Software Serial - Syncing two sensors to make a tx and rx beacon
theyre roughly 15 cm apart


15cm substantially less than the time it takes to send the second device its command at 9600 baud (2 bytes, probably 20 bits counting framing, around 72 cm)  

As a result you are likely missing the pulse, and perhaps catching some timeout, or even a cached response string from a next-to previous command which measured the previous pulse, including the time between pulses. 

To operate that close, you will need to either use dedicated trigger/detect wires, or start the receiver before you transmit and try to subtract the delay from the time you started the receiver until the time when you transmit.

Beware that usage of software serial, as well as buffering of serial in general may introduce variable latency in your timestamping of the serial communications.  Ideally for something like this you would use a non-buffered implementation - the timing of serial data itself is potentially precise to a fraction of the baud rate, though we don't know how it is implemented on the sensor end.