I have a mimaki but it sounds like the problems I encountered years ago sound similar. There’s 3/4 things I need to do to make sure it cuts ok.
1, as others have stated, make sure the media is inside the two pinch rollers on the edge of the media. (As per my mimaki, it has 1-6 so the media needs to be between 1 and 6)
2, whenever my sensor found the bottom two marks then sortve hovered over the third and failed, I found that it was because the media was a bit too short on the top edge and the media sensor was seeing a little bit light and thinking the sheet wasn’t long enough to cut - sorted that by putting a little bit masking tape over that sensor before I start cutting jobs.
3, we used to get the “cut data is outside the print width” a lot when we tried to cut. Basically the same problem as #1. We can get around that on the PC by changing the media width - my sheets are only 54” but I just tell it the sheet is 64” on the pc and then it runs no problem.
4, can you alter the registration marks in settings somewhere? I can extend the length of them and the thickness - this may help.