AVR Freaks

F_CPU doesn't set CPU speed, it just serves to inform the program and libraries of the current CPU speed. As mentioned by kabasan, the RTC doesn't necessarily use the same clock as the system.

You setup the clock sources separately. For example to set a 3.33MHz system clock:

I think it's defined somewhere inside the Start mess (yeah, it's in config/clock_config.h). However, since you are picking specific init functions and not the whole thing, you should define F_CPU yourself.

"Software timers"? That's pretty vague. I have no idea how you are implementing them...

Seems you are registering callback functions to some kind of system tick interrupt, that will then call them at specific times? In that case, the registered callback functions need to be called somewhere in the timer ISR.

What can I say? Remember, all global variables used inside ISRs need to be volatile. In particular, the array

TmrTbl[]

where you seem to be registering callbacks, needs to be volatile. I can only guess, since you didn't show the definition of this array.

So is this function being called regularly, as the library you are using expects? If so, from where? From the ISR or from main()?

/*
*********************************************************************************************************
												vTmrSignalTmr
*/

	/*! This function is called by the main program approx. every 10ms.  This function is thus
        responsible for counting the number of clock ticks per 1/10 second.  When 1/10 second
        elapses, this function will signal the timer manager task. TMR_DLY_TICKS must be set
	    to produce 1/10 second delays

      \param - nothing
      
      \return - nothing
    */ 

/*********************************************************************************************************
*/
void  vTmrSignalTmr (void)
{
    uTmrTickCtr++;
    if (uTmrTickCtr >= TMR_DLY_TICKS) {
        uTmrTickCtr = 0;
        vTmrTask();
    }
}

Remember that, if you end up calling it from the RTS overflow ISR, the global variables used must be volatile.

So this part may need to be changed:

/*
*********************************************************************************************************
*                                          GLOBAL VARIABLES
*********************************************************************************************************
*/

//! Table of timers managed by this module
TMR       TmrTbl[TMR_MAX_TMR];   

to

/*
*********************************************************************************************************
*                                          GLOBAL VARIABLES
*********************************************************************************************************
*/

//! Table of timers managed by this module
volatile TMR       TmrTbl[TMR_MAX_TMR];