Moti,
I think you have misunderstood how the timers works.
TMR_StartIntervalTimer() will start a timer, that calls the callback function (IntervalTimeoutHandler() in your code) every time X milliseconds have occoured ( TmrMinutes(1) in your case).
The TMR_StartIntervalTimer() is not a "blocking mode" delay function as you seem to be using it for.
Please try reading chapter 3 in the Freescale platform reference manual as it explains how the timers are used.
/Mads