Millis() is Not Working

I have a sketch that uses two timers using millis() from a library I created to keep time. The timers seem to be working correctly, but when I print the start time of each timer, it is clearly wrong.

E.g. the timer is set to run for 3 seconds. When I start the timer the first time, it reads that it started at 0. The next time I start the timer, right after it has finished running once, it reads that it started at 2 seconds. This should not be possible.

I have even tried timing it on my phone, and have seen the timerStart value read 5 seconds, when the sketch has been running for 10.

Does anyone have any idea what could be going wrong? Code below.

Here is the library's .h file:

#ifndef Timer_h
#define Timer_h

#include <Arduino.h>

class Timer {
  public:
    Timer(unsigned long timerLength);
    unsigned long timerStart;
    unsigned long timeElapsed;
    boolean isFinished = true;
    boolean timerStarted = false;
    void startTimer();
    void checkTimer();
  private:
    unsigned long _timerLength;
};

#endif

Here is the library's .cpp file:

#include <Arduino.h>
#include <Timer.h>

Timer::Timer(unsigned long timerLength) {
  _timerLength = timerLength;  
}

void Timer::startTimer() {
  if (!timerStarted) {
    timerStart = millis();
    timerStarted = true;
  }
}

void Timer::checkTimer() {
  timeElapsed = millis() - timerStart;
  if (timeElapsed >= _timerLength) {
    isFinished = true;
    timerStarted = false;
  } else {
    isFinished = false;
  }
}

And here is part of my sketch code, where the timerStart value is wrong:

#include <Timer.h>

Timer breathTimer(3000);
Timer betweenTimer(1000);

// this part determines if a turbine is spinning or not
SIGNAL(TIMER0_COMPA_vect) {
  uint8_t x = digitalRead(FLOWSENSORPIN);

  //if the turbine is spinning
  if (x == HIGH) {

    //start the breath timer
    if (betweenTimer.isFinished) {
      if (breathTimer.isFinished) {
        Serial.print("Breath Timer Started @ ");
        Serial.println(breathTimer.timerStart);
      }
      breathTimer.startTimer();
    }
  }
}

void setup() {
   Serial.begin(9600);
   pinMode(FLOWSENSORPIN, INPUT);
   digitalWrite(FLOWSENSORPIN, HIGH);
   betweenTimer.isFinished = true;
}

void loop() { 

  // check the breath timer
  if (breathTimer.timerStarted) {
    breathTimer.checkTimer();
    if (breathTimer.isFinished) {
      Serial.println("Breath Timer is Finished");
      betweenTimer.startTimer();
      Serial.println("Between Timer Started");
    }
  }

  if (betweenTimer.timerStarted) {
    betweenTimer.checkTimer();
    if (betweenTimer.isFinished) {
      Serial.println("Between Timer is Finished");
    }
  }
}