Combining high speed buses with stop mode and avoiding race conditions?

[arnold_w]

I working with the STM32F446-microcontroller and my project is using a simple home-made task scheduler: 

while (TRUE) {
    if (0 < numQueuedTasks(TASK_LOW_LEVEL_DRIVERS)) {
        handleNextTask(TASK_LOW_LEVEL_DRIVERS);
        continue;
    }
 
    if (0 < numQueuedTasks(TASK_HIGH_LEVEL_USER_EVENTS)) {
        handleNextTask(TASK_HIGH_LEVEL_USER_EVENTS);
        continue;
    }
 
    if (0 < totalNumQueuedTasks) {
        continue;
    }
 
 
    if (isAnyTimerRunning()) {
        enterSleepMode();
        continue;
    }
 
    if (0 < totalNumQueuedTasks) {
        continue;
    }
    
    enableExtWakeupInts();
    enterStopMode()
    disableExtWakeupInts();
}

I am using several buses and communication protocols (CAN, SPI & UART) and in order to wake up when there is traffic, I enable external interrupts on the appropriate pins (CAN Rx, SPI chip select and UART Rx) before I go to sleep. However, this approach isn't working well, if I get a bus-interrupt at line 25, then I will queue a TASK_LOW_LEVEL_BUS task, but it won't be serviced because the microcontroller will soon enter stop mode. How can I solve this? I guess in my interrupt routines I could somehow read where the program counter is destined to return to and if it's greater than line 20 then it should be manipulated to line 1 instead. But it seems like a hacking solution, can anyone think of a cleaner solution?