Normally I don't investigate until a complete program is posted, but this seemed so simple, so why not....
I drew this in the design tool.

Here's the code I tried. It does the same noteOn & noteOff sequence, first with the gain set to 0.75, then with the gain at 0 and changed to 0.75 after 80ms. It also pulses 2 digital pins, so I can easily see when the code is running with my oscilloscope.
Code:
#include <Audio.h>
#include <Wire.h>
#include <SPI.h>
#include <SD.h>
#include <SerialFlash.h>
// GUItool: begin automatically generated code
AudioSynthWaveformSine sine1; //xy=217,242
AudioMixer4 mixer1; //xy=400,266
AudioEffectEnvelope envelope1; //xy=577,269
AudioOutputI2S i2s1; //xy=768,273
AudioConnection patchCord1(sine1, 0, mixer1, 0);
AudioConnection patchCord2(mixer1, envelope1);
AudioConnection patchCord3(envelope1, 0, i2s1, 0);
AudioConnection patchCord4(envelope1, 0, i2s1, 1);
AudioControlSGTL5000 sgtl5000_1; //xy=622,339
// GUItool: end automatically generated code
void setup() {
pinMode(3, OUTPUT);
pinMode(4, OUTPUT);
AudioMemory(20);
sgtl5000_1.enable();
sgtl5000_1.volume(0.75);
mixer1.gain(0, 0);
mixer1.gain(1, 0);
mixer1.gain(2, 0);
mixer1.gain(3, 0);
sine1.frequency(1000);
sine1.amplitude(0.9);
}
void loop() {
mixer1.gain(0, 0.75); // first trial with gain at 0.75
digitalWrite(3, HIGH);
delay(50); // pulse pin 3 before normal test (trigger oscillscope)
digitalWrite(3, LOW);
envelope1.noteOn();
delay(160);
envelope1.noteOff();
delay(500);
mixer1.gain(0, 0); // second trial with gain starting at 0
digitalWrite(4, HIGH);
delay(50); // pulse pin 4 before gain change test
digitalWrite(4, LOW);
envelope1.noteOn();
delay(80);
mixer1.gain(0, 0.75); // set gain to 0.75 about 80ms after noteOn
delay(80);
envelope1.noteOff();
delay(500);
}
This is the result I see on my scope.

It certainly seems to be working. The 2nd waveform indeed starts with nothing because the gain is 0, but then when the gain is set to 0.75, it looks exactly the same as the first waveform except the first 80ms are missing.
Here is the hardware setup on my workbench with the oscilloscope probes connected.

Best I can conclude is this case does indeed work properly. If you still feel there is a bug here, obviously I can't reproduce it unless you post a complete program I can run here to observe the problem.