careful doubling up the cutcontour line. I had that happen by accident once and when it went to cut, the lines not only did a double cut but the double cut paths were stopping and starting at odd places... and in the end, I never got a full cut to go through. I had to disect the file, reset the cut line as a completely new layer (not a copy, paste in front; but physically recreated the cut line) - deleted former cut line, saved as a new filename and finally got what I needed to go through.
I dont understand how the bottom is cutting properly but the top is not. Can you remove your blade to see if its possibly gummed up, causing it to not pivot properly? That was one of the issues that arose with our Graphtec.
Good Luck!