I found the issue. The issue is a change in CM5. This is going to have to be a change for our faculty to know in their syllabi for art students. The change in CM5 from CM4 is this. On CM4 in illustrator your art board could be say 24 x 24 and in the file you know to add 2" right and left with no artwork in that space to allow for the grit rollers (1” each side) and an extra inch for the registration marks. If you loaded the sheet into the cutter regardless of the poll size in CM4 it would just find the marks, and contour cut the file. In CM5 Apparently the art board is now being considered when sending the cut job. So, for the last 13 years I’ve always done 24” wide by x length. So, when I had this issue, I assumed it was an issue in CM5, which it is, and kind of I guess, isn’t. So I adjusted my art board to 22” wide by 32” tall. Sent the file to our Canon ImagrPrograf 4000s on a paper size of 24 x 32 so the printer understood the file. Then in illustrator I left the art board at 22”. The poll size on the cutter is 22.5”. When I sent the file, it allowed it to find the marks and cut. But WHY change that setting after 12+ years??? UGH!!.
I think this is also why the cutting page was rotating 90° I think the software doesn't know what to do with margins like that and just rotates it to fit. which kind of makes sense.
thanks all for the adivce, and options. Now if I can only find a 2.x firmware for my Graphtech FC8600-60 to update so the version 3 firmware will take. but that's a different issue.
Thanks again all.