I've used a few older 120 cameras (including the Mamyia 645) and not had the problem that you mention, but i do know with some RFH holders if you start the roll off with film laced into the take-up reel incorrectly (such as going over the spool instead of under) the initial spacing, if not all the spacing, can be off.
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:
I have a very old and worn Omega Rapid back I start past the red dot a little to fix spacing between frame one and two. Not a film issue, as I don't have to do it with my other two backs, but this one really needs a CLA.