change your cutter marks... easiest fix.
There's a type1 and a type2 (one's like a box, and the other's inverted like a .psd artboard, just figure out which type flexi outputted as when you set your cutcontour and change the settings in your cutter to match....
I believe its function>setup>markdetect, but I've only found it by digging around the function menu on the cutter when i changed mine.