AVR ATmega32U4 Timer compare interrupt not triggering?

I tried to create a CTC timer interrupt on my ATmega32U4 leonardo board. When I continuously check the value of OCF1A I have no problem detecting when the output reaches the desired value, however once I move the code into an interrupt, the interrupt never triggers.

Here is the atmega32u4 datesheet

Timer setup:

#include <avr/io.h>

void setupTimer()
    TCCR1B |= (1 << WGM12); // CTC mode
    TCCR1B |= ((0 << CS10) | (0 << CS11) | (1 << CS12)); // set up prescaler
    OCR1A = 6249; // 100 ms set up output compare value for interrupt
    TIMSK1 |= (1 << OCIE1A); // enable interrupt on clock compare

The loop that works:

for (;;) {
    if (TIFR1 & (1 << OCF1A)) {
        PORTC ^= (1 << PORTC7);
        TIFR1 = (1 << OCF1A);

The interrupt that does not work:

#include <avr/interrupt.h>

    PORTC ^= (1 << PORTC7);

I must be missing something as from what I have seen in the tutorials the above code should work. One interesting observation here is that if I have both the loop and the interrupt in my code at once if I call sei(), the LED does not blink as if the OCF1A register was cleared prematurely.
I'm pretty sure it is irrelevant in this case but the fuses are as follows: E:CB, H:D8, L:FF.

I use avr-g++ to compile and the code is spread out between several files.

iceng15 days ago

I only like to set interrupts in ML but you have to understand 3 to 4 registers...

Compilers are written by starving code monkies that are time limited and switched around, No wonder they trip up..... It could be you . . . Naaw its the code monkies...