Pretty much what you said -- more set up time. More dogs, more 1x's with duplex nails or screws, etc. And then you have to move them when they're in the way. There is no magic bullet. It does help to flatten where it is bearing -- even if you have to shim it with wedges, it's more stable than a round.
Another trick on really floppy stuff, like a small pole rafter is to cut a 1x to run to the ground and tack it into the end grain -- that's a slight adaptation of a trick Will Truax showed us last time he worked with us. That keeps the floppy ends from bouncing too much.
And now a few questions --
What size logs?
what species?
how dry/green?
what size timbers are you getting out of them?
