Arduino hardware interrupt reliability issue - arduino

Question

This may seem like a foolish problem and maybe its description is not the best I could have devised.
I am making a velocity sensor that uses two IR beams to calculate velocity based on the time it takes to break both beams.
I have two testing methods.
My hand (5-10 m/s)
A high speed cannon (30-60 m/s).
I have ruled out that it's a problem with the signal from the IR beams with an oscilloscope, when the code fails/works the data is identical on the scope.
My problem is that my code works when I use my hand, but still irregularly fails, while it fails more often at high speed. All the conditions are the same in both scenarios. What could be the issue?
#include <SPI.h>
#include <SD.h>
#include <LiquidCrystal.h>
const int rs = 9, en = 8, d4 = 7, d5 = 6, d6 = 5, d7 = 4;
LiquidCrystal lcd(rs, en, d4, d5, d6, d7);
File root;
int fileNo = 0;
String currentFileName;
const int CS = 10;
const byte interruptPinStart = 2;
const byte interruptPinFinish = 3;
volatile unsigned long int startTimeMillis = 0;
volatile unsigned long int stopTimeMillis = 0;
volatile unsigned long int startTimeMicros = 0;
volatile unsigned long int stopTimeMicros = 0;
volatile unsigned long int microsDifference = 0;
volatile unsigned long int millisDifference = 0;
int launchNo = 0;
float currentVelocity = 0;
volatile boolean started = false;
String inputString = "";
boolean stringComplete = false;
const int txLed1 = 14;
const int statusLed1 = 15;
const int statusLed2 = 16;
volatile boolean triggerDone = false;
float velocity = 0;
String temp;
unsigned long int lockout = 0;
boolean lockedOut = false;
boolean fileFail = false;
int testNo = 0;
void setup() {
inputString.reserve(200);
pinMode(statusLed1, OUTPUT);
pinMode(statusLed2, OUTPUT);
pinMode(txLed1, OUTPUT);
Serial.begin(9600);
while (!Serial) {
;
}
lcd.begin(16, 2);
pinMode(interruptPinStart, INPUT);
attachInterrupt(digitalPinToInterrupt(interruptPinStart), startTrigger, RISING);
pinMode(interruptPinFinish, INPUT);
attachInterrupt(digitalPinToInterrupt(interruptPinFinish), stopTrigger, RISING);
Serial.print("Initializing SD card...");
if (!SD.begin(CS)) {
Serial.println("initialization failed!");
return;
}
Serial.println("initialization done.");
root = SD.open("/");
newDirectory(root);
Serial.println("done!");
lcd.clear();
lcd.print(currentFileName);
tone(txLed1, 38000);
}
void loop() {
int millsDiff = millis() - stopTimeMillis;
if (triggerDone) {
lockedOut = true;
Serial.print("Micros Diffrence: ");
Serial.println(microsDifference);
Serial.print("Millis Difference: ");
Serial.println(millisDifference);
float millDiff = (float) millisDifference;
float microDiff = (float) microsDifference;
if (microDiff > 0) {
velocity = (float) 0.09 / (microDiff/1000000);
testNo++;
temp = String(launchNo) + "%" + String(microsDifference) + "%" + String(velocity);
if (velocity > 10.0) {
root = SD.open(currentFileName, FILE_WRITE);
if (root) {
root.println(temp);
root.close();
Serial.println(temp);
launchNo++;
} else {
Serial.println("error opening file, " + currentFileName);
fileFail = true;
}
}
if (fileFail) {
lcd.clear();
lcd.print("File Error");
lcd.setCursor(0, 1);
lcd.print("Vel " + String(launchNo) + ": " + String(velocity) + " m/s");
fileFail = false;
} else {
lcd.clear();
lcd.print("Test Number: " + String(testNo));
lcd.setCursor(0, 1);
lcd.print("Vel " + String(launchNo) + ": " + String(velocity) + " m/s");
}
}
triggerDone = false;
Serial.println("Test Number: " + String(testNo));
}
if (digitalRead(interruptPinStart) == LOW) {
digitalWrite(statusLed1, HIGH);
} else {
digitalWrite(statusLed1, LOW);
}
if (digitalRead(interruptPinFinish) == LOW) {
digitalWrite(statusLed2, HIGH);
} else {
digitalWrite(statusLed2, LOW);
}
}
void startTrigger() {
startTimeMicros = micros();
startTimeMillis = millis();
volatile int diff1 = startTimeMicros - startTimeMillis;
volatile int diff2 = startTimeMillis - stopTimeMillis;
if (diff2 > 200) {
if (started == false || diff1 > 1000) {
started = true;
triggerDone = false;
}
}
}
void stopTrigger() {
stopTimeMicros = micros();
stopTimeMillis = millis();
microsDifference = stopTimeMicros - startTimeMicros;
millisDifference = stopTimeMillis - startTimeMillis;
if ((millisDifference > 0 && millisDifference < 800) && started) {
microsDifference = stopTimeMicros - startTimeMicros;
millisDifference = stopTimeMillis - startTimeMillis;
started = false;
triggerDone = true;
}
}