I've encountered this problem. What can happen on long print cuts is that the vinyl stretches and the registration marks will print slightly misaligned from each other, that's why it will fail in the same spot. To check if that's the case just roll out your print and measure from the first reg marks to the problems ones, if you get differing measurements then that's likely your issue. Even an 1/8th inch difference can cause it to fail.
The only fix I know is to take the reg marks off a print that had no problem cutting and lay those down carefully and evenly over the bad reg marks in a strip, the key is to line it up near perfect to the first reg marks printed and not put the vinyl to hard as you're laying it down as you'll just encounter the same problem of misaligned marks. It's a pain and takes a bit of time if you're not confident, but I've had surprising success with this fix.
If it's a common thing that's happening with you're prints cuts, then I would say its one of three possibilities, you're printer isn't feeding evenly, something is wrong with you're Graphtec sensor or the black of the reg is to dull, or when you build your reg marks in adobe or whatever program, using the cutting master plugin, they are not perfectly aligned across from each other. I would say check your files first and make sure the regs marks are all in alignment. If they are, do what I suggested and measure the marks that printed and see if they are off.
If none of the works, then I dunno what to tell ya, cause that's weird,