Switch from Teensyduino 1.36 to 1.41 causing issues

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Hello all, I've been using a teensy 3.2 to stream audio from an acoustic microphone and contact microphone as stereo to audacity through USB, and to save the audio to an SD card at the same time. I wrote the code in Arduino 1.6.12/Teensy 1.36. When I transferred the sketch over to Arduino 1.8.5/Teensy 1.41 the audio stream which was previously acoustic mic on one channel, contact mic on the other started streaming the acoustic microphone at a higher pitch to both channels. Not sure why the sketch doesn't work on the new version of the IDE, not sure how to fix it.
See forum rule at top of page: Always post complete source code & details to reproduce any issue!
Not sure why the sketch doesn't work on the new version of the IDE, not sure how to fix it.

I don’t know either. There certainly hasn’t been any change which would explain this problem. It must be something subtle, maybe a new bug, maybe something in your code depending on the old version in some unanticipated way. Subtle problems aren’t the sort of thing anyone can guess with only a description. If you want me to investigate, you really do need to compose a small but complete program I can run on a Teensy here.
Hi guys, sorry about not posting code originally, had to pare down the code as much as possible, as this project is for my work and I couldn't just post the whole sketch as it was. Below is the part of the code relating to the issue I'm having.

//Teensy 3.2, Teensyduino 1.36, Arduino 1.6.12
//USB Type: Audio
//96 MHz optimize speed (overclock)

#include <Audio.h>
#include <Wire.h>
#include <SPI.h>
#include <SD.h>
#include <SerialFlash.h>
#include <TimeLib.h>

//BC127 I/O
#define play_pause 4
#define streaming 5

//BC127 I2S Pins
#define bt_clk 9
#define bt_out 13
#define bt_sync 23

//VREG pin
#define vreg 15

#define blue_led 20

//SparkFun Navigation Switch
#define steady_state 18
#define activate 19

//Switch activation/verification
int switch_state;

//Switch press debounce
long t = 0;
long debounce = 1000;

//Audio streaming
AudioInputI2Sslave       i2s_slave1;     //xy=105,63
AudioOutputUSB           usb1;           //xy=439,164
AudioConnection          patchCord3(i2s_slave1, 0, usb1, 0);
AudioConnection          patchCord4(i2s_slave1, 1, usb1, 1);

void setup() {
  pinMode(steady_state, INPUT_PULLUP);
  pinMode(activate, INPUT_PULLUP);
  pinMode(streaming, INPUT);
  pinMode(vreg, INPUT_PULLUP);
  pinMode(play_pause, OUTPUT);
  pinMode(blue_led, OUTPUT);

  digitalWrite(play_pause, LOW);

  //Start serial bus and set rate

  //Audio Memory Allocation

void loop() {
  switch_state = digitalRead(activate);
  if (switch_state == HIGH && millis() - t > debounce) {
    //Flicker play_pause pin until BC127 is streaming
    if (!digitalRead(streaming)) {
      while (1) {
        digitalWrite(play_pause, HIGH);
        digitalWrite(blue_led, LOW);
        digitalWrite(play_pause, LOW);
        digitalWrite(blue_led, HIGH);
        if (digitalRead(streaming)) break;
    t = millis();

So the device I'm working on is a teensy 3.2, to which is attached a BC127 Bluetooth receiver which receives the audio from 2 microphones attached to the paired transmitter. Channel 1 (Left) receives the audio from an acoustic microphone, Channel 2 (Right) receives the audio from a contact microphone, and both are streamed over usb to the computer (using audacity). I have a Sparkfun navigation switch attached so I can flicker the play/pause pin of the BC127 until it starts receiving audio from the transmitter. Running in (Arduino/Teensyduino) 1.6.12/1.36, everything is fine, I get each mic on the corresponding channel of the stereo stream in audacity. Running in 1.8.5/1.41 I get only the high end of the acoustic microphone on both channels. Hope I've provided enough info, I really appreciate the help.
Oh, now I can see I2S slave mode is part of this equation. Wouldn't have guessed that.

Can you give me a link or details about the I2S hardware you're using?
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