Python Audio Transfer Through Lasers
Did you do a sanity check by listening to the sound files (both transmit and receive), or viewing the waveforms with an audio editor, to see if they roughly sound or look the same?  That way you can narrow down the problem to channel induced errors versus your software analysis.
Your decoding/demodulation software will need a synchronization method that can determine and track the times that the audio signal changes from one frequency of modulation to another, then you will need to separately test this synchronization method for offset errors.
I'm currently working on a project that has been relatively easy, up until now. The underlying project is to transmit data/messages over lasers using audio transformation.
In a nutshell the process is currently like this

The user enters a message
Message is turned into binary
For each 1 and 0 in the binary message, it plays a corresponding tone to signal which is which, in my case 250hz for a 1 and 450 hz for a 0.
The outgoing tone is sent over a stereo cable to an audio transformer rigged to a laser
A solar panel acts as a microphone and records the incoming "sound" as a file
It them plays the file back and reads off the tones and tries to match each 250 and 450 hz to a 1 or 0 (which is where my issue lies).

Up until the actual processing of the sound is fine, my current issue is the following. 
I play the tones each for x time, on the receiving end it is recorded for y time, y time is cut sampled many times and then analyzed sample by sample which then logs each frequency. This is inefficient and inaccurate. I have had many issues regardless of the time I play the tones for it often hears a tone twice or doesn't hear it at all, which completely throws off whole messages.
I have tried to match the rate at which it samples with the time each tone plays, but unless aligned accordingly it does not work. I've only had a few successful tests for messages like 'test' and 'hi'. I have already looked into bpsk and fsk, but I feel as if I'm already doing something like it but that I have a bad receiving end to decipher it all.
This is all written in Python and I'd be very grateful for any tips, suggestions, or possible implementations that you can provide. Also for tone emission I'm using pyaudiere and for recording I'm using pyaudio.
Thanks!
-Steve