I've had that problem but not with the Saginaw. When I had it, it was because I had the wrong shifter(with Muncie). Got the right shifter and put the console in the right place and it was fixed.
The 69 only came with the m20 and the m21 Muncies. If the 'throw' on the Saginaw is different then the correct console shifter wouldn't work. I haven't seen any shifter offered for the Saginaw that works with the console.