Want to stop milliseconds from increasing

Question

I'm trying to create a timer app, but I have this problem with milliseconds.

When someone activates the timer I save the current milliseconds and then I just this to get the difference between them

long startMillisecond; long i = System.currentMillisecond() - startMillisecond

and then I display this variable i with some other code. However when I pause my program my variable i stays on the right value, but when I start the program again I get the "wrong" value since System.currentMillisecond() keeps increasing (internally), so it looks like it "jumps" over a couple of seconds

Example: Start app > variable i = System.currentMillisecond() - startMillisecond is equal to 0. And now if I pause for 5 seconds and then resume my variable i have the value of 5.

Anyone knows how I can let it be on the same value when I paus?

EDIT. Here is my code for my run function

String tempstring;

int millisec,sec,min,hour;

Handler handler;
Runnable runnable;

SensorManager mSensor;
Sensor accSensor;

Button startButton,stopButton,resetButton;
TextView whiteplayertime,blackplayertime,xt,yt,zt;

public void StartTimer(View view){
    mSensor.registerListener(this, accSensor, SensorManager.SENSOR_DELAY_NORMAL);
    handler = new Handler();
    runnable = new Runnable() {
        @Override
        public void run() {

           if(startmillisec <= 0){
                startmillisec = System.currentTimeMillis();
            }        
            tempmillisec = System.currentTimeMillis() - startmillisec;

            millisec = tempmillisec;
            millisec /= 100;
            millisec = millisec % 10;
            sec = TU.MILLISECONDS.toSeconds(tempmillisec);
            sec = sec % 60;
            min = TU.MILLISECONDS.toMinutes(tempmillisec);
            min = min % 60;
            hour = TU.MILLISECONDS.toHours(tempmillisec);
            hour = hour % 24;
            tempstring = String.format("%02d:%02d:%02d:%d",hour,min,sec,millisec);
            whiteplayertime.setText(tempstring);
            handler.post(this); //This is the last in the code
        }
    };
    handler.post(runnable);

Answer 1

Simple save elapsed from the last stop value and save in a variable if the timer is ongoing or not.

public MyTimer {
    private long startTime;
    private long elapsed;
    private boolean running;

    public void start() {
        startTime = System.currentTimemillis();
        running = true;
    }

    public void stop() {
        elapsed = elapsed + System.currentTimemillis() - startTime; 
        running = false;   
    }

    public long getElapsed() {
        if (running) {
            return elapsed + System.currentTimemillis() - startTime;
        } else {
            return elapsed;
        }
    }
}