The problem I was having was when i started offsetting body parts of the animation from the main key poses i had set in the cycle.
Lets say I have a breathing cycle and want to offset the head to trail slightly behind the rest of the body movement. If I'll try setting a key 3 or 4 frames in from the first one, and dip the head down a bit, and the raise it slightly a few frames after the middle keyframe.
What happens then though is that i can't line up the start and end keys to smoothly cycle the head after doing this. I've tried all different kinds of combonations of the curve editor, but there will still be a hiccup (and yes i've tried removing the duplicate last keyframe as well so that its not playing both the first / last keyframe twice.
Anywhoo, so the only way i've found to work around this hiccup, is to make the cycle from frames 30-90 lets say. Then to repeat the cycle once at the beginning and once at the end. Then offset the head, but change the looping playblack area to 30-90. This makes it so the head cycles perfectly. (there's just no actual key at 30 or 90 for the head).
And thus the only way to export it properly is to export the entire 120 frames, at 30fps and to delete frames 1-29 and 90-120.
i can try and make a video recording of the issue if its not clear how i described it.