Once you start counting instruction cycles, you will realize how they all add up to get you to the 30uS extra that you see. A call takes 2 cycles, a return another 2, and so on.

I am a bit curious about your application and how you achieve colour fading. According to what you have shown here, you seem to be lighting the leds one behind the other with a fixed pause in between. I do not know why you have it that way, but, I would think it would be better to have them work in tandem unless you want just 1 led on at a time.

Why not use 3 PWM channels one per colour to control the intensity of each?
Now, the refresh rate for all the channels will be the same, but, the on-time for each led will be decided by its on-time variable.

Would this work for you?