Ironknees,
I have had a similar experience as you. My Marlin GG in 45/70 shoots cloverleafs at 50 yards with a peep sight, but my microgroove 30-30 shoots well over an inch at 50 yards with a scope and factory ammo. The 30-30 exhibits quite a bit of vertical stringing as well.
I studied the rifling in my 30-30, and it's rough as a cob. The chatter marks in the muzzle are VERY apparent. It's a candidate for fire lapping after I make a few other modifications.
I've been reading McPherson's book "Accurizing the Factory Rifle." He goes into a great amout of detail as to the causes of inaccuracy of some of the Marlin lever action rifles, and the gives fairly simple antidotes for each of the gremilns.
The crown, the way the magazine tube is held, the forend and butt bedding, the extractor claw, and the way the barrell is mated to the receiver can all cause what you're experiencing.
If you are able, try to pick up a copy of the book. Even if you don't do any of the modifications described in the text, it's still interesting reading about the various effects of the way these rifles are put together.
By the way you describe the problem, it sounds like the ammo is not the problem. It's most likely one of the items that McPherson addresses in his book.
Hope that helps...
The Blade