When I was scanning for Al with his Ricoh scanners, I
had to do the page at a
time trick. I prepared each manual by fanning it, and making sure each page
was free, then just fed each page. Sadly not being able to put in a manual
and go away.
<sigh>.. I had a feeling that was the only reliable answer. It's
slightly less painful than repeatedly laying the pages into a flatbed
scanner, though.
It probably doesn';t save any time or work, but what happens if you turn
every other page through $\pi$ (keeping it the same face up) so that the
holes/'cones' can't interlock throughout the stack. And then convince the
software to roate every otehr scan back again.