Hi Sam,
Your situation sounds so familiar, but I doubt it has the same cause as ours. We have struggled for years with native morning glory vines on any young trees. The vines are so vigorous and plentiful that they are capable of climbing a tree, pulling it down with the vine weight, and tethering it to the ground. We lost lots of central leaders (and trees, outright) in our orchard because we were swamped with other work at a time when we needed to be bushwhacking morning glory vines. While they are still a huge problem in the orchard, aside from watching any re-plants closely, the loss of central leaders is no longer a huge issue for us now that the trees are in their 12th year out there.
As you described, in cases where a central leader has been pulled down, the tree will put out some vigorous new growth, sometimes a water sprout, sometimes not, right where you'd want a central leader if you weren't still mourning the loss of your old one. In the past we've either pruned to favor that new central leader sprout or given up the central leader system altogether and pruned to create a double leader tree, etc. However, a couple years ago, we started playing around with tying up and tethering the old central leader on some of our older trees where we had just sort of let that leader go, cattywampus, no longer particularly central, but growing dominantly enough that we couldn't bear to prune it out. We use 12-foot t-posts to do this, and so far, it's worked great. Since you're dealing with young trees, it should be even easier for you to get back on the right path.
As I said, I can't imagine that morning glory vines were your problem (you would have known it), so I'm scratching my head at your potential cause. Don't know how many trees you have -- could it be an animal issue (something too heavy for the tree climbing it or perching on it for prolonged periods)? Otherwise, my vote would be for wind. There's nothing much between us and the Blue Ridge Mountains but a barbed wire fence, and we've got the wind. We don't/didn't stake our trees, but try/tried to plant "into" the wind (position the tree such that even the slightest deviation from straight is pointing into the wind to help compensate being blown back in the opposite direction with the typically prevailing wind). We also have a fair amount of windblown trees in our orchard where, again, lack of time, meant we didn't correct their growth in any way before it became permanent, and we do have some pretty good leaners out there that we've worked with over the years, to try and correct to some extent. But to your statement that you'd expect all the trees to have been blown similarly, I would say, logically, yes, that's what I would have expected, too, but you'd be surprised. Depending upon your topography, the wind direction may be changing more frequently than you'd think, and in the end, some trees go one way, others go another.
Kordick Family Farm
Westfield, NC
Zone 7a