Ok, Paul, here I am, ready to post.
You guys with two rim locks must be moma's boy's with no sense of adventure...
(Just kidding).
On the balance issue, those who still run the Reno to Vegas event balance the wheels front and rear, but this is because of the sustained HIGH SPEED running. If you're not running sustained high speeds, balancing should not be necessary.
With that said, you probably have another problem relating to the rim. I think You mentioned you checked the side-to-side alignment of the rim, but don't remember you indicating you checked the outside of the rim in relation to the hub. You can check this easily by clamping a srewdrive to the swingarm and rotate the tire while watching the rim's movement in relation to the screwdriver. I would not be surprised to hear that the rim is not centered on the hub. This is not real tough to fix, so just post up if that is a problem.
Finally, in my oppinion, balancing an offroad rim is a waste of time, as I do not believe any weights installed can stand the abuse of the offroad environment. As for two rim locks, I stay with one, as it makes for a faster tire change. With all the racing and riding, I have had two flat tires, both on the front. However, even with only one front rim lock, I still rode just under 90 miles in a California National Hare & Hound without a problem...OK, the bike was a little squirrelly in the deep sand, but that was all the more reason to keep her pinned.
Rick
I'll be curious to hear what you find as you investigate further.