Arduino MIDIUSB button stops working when I light LED on push - button

Question

I have worked on a sketch for my Arduino Micro (not Pro Micro) that includes 4 mini arcade buttons with integrated LEDs. When I upload my sketch without the LED logic, everything works correctly but when I upload the sketch with the LED logic, the button press is recognized but not the note on/off message.
Does anyone see what would stop this from working?
Original Sketch
#include "MIDIUSB.h"
#include "PitchToNote.h"
#define NUM_BUTTONS 4
const uint16_t button1 = 2;
const uint16_t button2 = 3;
const uint16_t button3 = 4;
const uint16_t button4 = 5;
const uint16_t buttons[NUM_BUTTONS] = {button1, button2, button3, button4};
const byte notePitches[NUM_BUTTONS] = {pitchC2, pitchD2b, pitchD2, pitchE2b};
uint16_t notesTime[NUM_BUTTONS];
uint16_t pressedButtons = 0x00;
uint16_t previousButtons = 0x00;
uint16_t intensity;
void setup() {
for (int i = 0; i < NUM_BUTTONS; i++)
pinMode(buttons[i], INPUT_PULLUP);
}
void loop() {
readButtons();
playNotes();
}
void controlChange(byte channel, byte control, byte value) {
midiEventPacket_t event = {0x0B, 0xB0 | channel, control, value};
MidiUSB.sendMIDI(event);
}
void readButtons()
{
for (int i = 0; i < NUM_BUTTONS; i++)
{
if (digitalRead(buttons[i]) == LOW)
{
bitWrite(pressedButtons, i, 1);
delay(2);
}
else
bitWrite(pressedButtons, i, 0);
}
}
void playNotes()
{
for (int i = 0; i < NUM_BUTTONS; i++)
{
if (bitRead(pressedButtons, i) != bitRead(previousButtons, i))
{
if (bitRead(pressedButtons, i))
{
bitWrite(previousButtons, i , 1);
noteOn(0, notePitches[i], 100);
MidiUSB.flush();
}
else
{
bitWrite(previousButtons, i , 0);
noteOff(0, notePitches[i], 0);
MidiUSB.flush();
}
}
}
}
void noteOn(byte channel, byte pitch, byte velocity) {
midiEventPacket_t noteOn = {0x09, 0x90 | channel, pitch, velocity};
MidiUSB.sendMIDI(noteOn);
}
void noteOff(byte channel, byte pitch, byte velocity) {
midiEventPacket_t noteOff = {0x08, 0x80 | channel, pitch, velocity};
MidiUSB.sendMIDI(noteOff);
}
LED Logic
#include "MIDIUSB.h"
#include "PitchToNote.h"
#define NUM_BUTTONS 4
const uint16_t button1 = 2;
const uint16_t button2 = 3;
const uint16_t button3 = 4;
const uint16_t button4 = 5;
const uint16_t buttonLed1 = 6;
const uint16_t buttonLed2 = 7;
const uint16_t buttonLed3 = 8;
const uint16_t buttonLed4 = 9;
const uint16_t buttons[NUM_BUTTONS] = {button1, button2, button3, button4};
const uint16_t ButtonsLEDS[NUM_BUTTONS] = {buttonLed1, buttonLed2, buttonLed3, buttonLed4};
const byte notePitches[NUM_BUTTONS] = {pitchC2, pitchD2b, pitchD2, pitchE2b};
int lastpress = 0;
uint16_t notesTime[NUM_BUTTONS];
uint16_t pressedButtons = 0x00;
uint16_t previousButtons = 0x00;
uint16_t intensity;
void setup() {
for (int i = 0; i < NUM_BUTTONS; i++)
{
pinMode(buttons[i], INPUT_PULLUP);
}
for (int i = 0; i < NUM_BUTTONS; i++)
{
pinMode(ButtonsLEDS[i], OUTPUT);
}
}
void loop() {
playNotes();
}
void controlChange(byte channel, byte control, byte value) {
midiEventPacket_t event = {0x0B, 0xB0 | channel, control, value};
MidiUSB.sendMIDI(event);
}
void readButtons()
{
for (int i = 0; i < NUM_BUTTONS; i++)
{
if (digitalRead(buttons[i]) == LOW)
{
for (int x = 0; x < NUM_BUTTONS; x++)
{
if (lastpress != i) {
digitalWrite(ButtonsLEDS[x], LOW);
}
}
digitalWrite(ButtonsLEDS[i], !digitalRead(ButtonsLEDS[i]));
lastpress = i;
bitWrite(pressedButtons, i, 1);
delay(2);
while (digitalRead(buttons[i]) == LOW) {
}
}
else
bitWrite(pressedButtons, i, 0);
}
}
void playNotes()
{
for (int i = 0; i < NUM_BUTTONS; i++)
{
if (bitRead(pressedButtons, i) != bitRead(previousButtons, i))
{
if (bitRead(pressedButtons, i))
{
bitWrite(previousButtons, i , 1);
noteOn(0, notePitches[i], 100);
MidiUSB.flush();
}
else
{
bitWrite(previousButtons, i , 0);
noteOff(0, notePitches[i], 0);
MidiUSB.flush();
}
}
}
}
void noteOn(byte channel, byte pitch, byte velocity) {
midiEventPacket_t noteOn = {0x09, 0x90 | channel, pitch, velocity};
MidiUSB.sendMIDI(noteOn);
}
void noteOff(byte channel, byte pitch, byte velocity) {
midiEventPacket_t noteOff = {0x08, 0x80 | channel, pitch, velocity};
MidiUSB.sendMIDI(noteOff);
}