Electronic – AVR and external crystals

This is a bad approach. Ideally you would measure a very large number of NOP commands - say, one million - instead of just one. I think that's the first foolish thing I can find. I would not be very surprised if your number changes right after you implement that change.

Also, can you view the disassembly of your C code? I wouldn't even try to judge the timing without seeing exactly what assembly code was generated from my C code. I would try to work backwards from the assembly to calculate what the execution time should be (via the instruction set manual you found). That way you can see if the scope measurement is off by a little or by a lot. A little might mean you made a math error. A lot might mean one of your assumptions is wrong.

It looks your MCU is running at 1MHz like alexan_e describes. Check your fuses - select external crystal as a clock source and unset CKDIV8 fuse.

Regarding your code - you are doing it wrong. You should use interrupts to detect timer events. In this particular case - an Output Compare Match interrupt.

You have to set your magic number to OCR1A and set bit OCIE1A in TIMSK register to enable the interrupt. Don't forget to provide timer1 overflow interrupt A handler in your code.

This way your code will not be stuck in closed loop while timer is counting. That's the beauty of using peripherals in MCU - they are trully running in parallel - while the timer is counting, the processor can do other usefull stuff or conserve power sleeping.

Please note, that you either have to reset the timer to 0 yourself in the interrupt handler or set timer to CTC mode (WGM12 bit in TCCR1B)