I have read the specifications on timers (KL26 Sub-Family Reference Manual) and partially got it to work but I still have a problem with the prescaling.

I would like to start a timer at a high resolution, e.g. 1Mhz/1us, and run this timer for a given time. Then I don't want an interrupt to be executed but instead check the Overflow flag.

Here is the code:

void setup() {
  // Initialize pins
  pinMode(14, OUTPUT);

  // Setup timer
  MCG_C1 &= ~0b010; // Disable IRCLK
  MCG_SC &= ~0b01110; // Divider = 1 => 4MHz
  MCG_C2 |= 0b001;  // IRCS. fast internal reference clock enabled
  // Clock source
  SIM_SOPT2 |= 0b00000011000000000000000000000000;  // MCGIRCLK

  // Prescaler: 4 -> 4MHz/4 = 1MHz => 1us
  TPM0_SC = 0;
  TPM0_SC |= 0b00000010;  // Prescaler /4 = 1Mhz
  TPM0_SC |= 0b00001000;  // Enable timer
  MCG_C1 |= 0b010;  // IRCLKEN = enabled

  // When this is reached the overflow flag is set.
  TPM0_MOD = 1000; // 1000us = 1ms

  // Loop: toggle a pin each time the timer elapses (overflows)
  bool out = false;
  while(true) {
    TPM0_CNT = 0;  // Start value for timer
    TPM0_SC |= FTM_SC_TOF;  // Clear overflow
    out = !out;
    digitalWrite(14, out);
    TPM0_CNT = 0;  // Start value for timer
    TPM0_SC |= FTM_SC_TOF;  // Clear pending bits
    // Wait on timer overflow
    while(!(TPM0_SC & FTM_SC_TOF));

The code above seems to work fine. With an oscilloscope I can see that pin 14 toggles. But unfortunately it shows 500us for the timer instead of 1000us what I had expected.

But even more strange: It doesn't even matter what prescaler I use. I can change the line to
 TPM0_SC |= 0b00000111;  // Prescaler /128
The output is still the same, i.e. the oscilloscoe still shows 500us.

What am I missing? Why is the prescaler not having any effect?