Is there any chance that you are mistaken about where the start mark line up indicator is on your inserts?

All of my 120 cameras line up properly (Mamiya 645, Mamiya C330/C220, Koni-Omega) but it is really hard to see the indicator on the Koni-Omega backs. I have more than once lost track of the indicator .

On the 645 inserts, the start mark is on the tab that holds the end of the film spool. You've probably already done this, but here is a link to the manual for the 1000s - see page 24/25:

http://www.mamiya.com/assets/pdfs/645/M645_1000S_v4.pdf

Matt