Yeah, I've been fighting this issue over the past few days, but on my Mac. After updating to macOS 12.3/Safari 15.4, the first bookmark I added in Safari on my Mac went to the top of the list and synced to my iPhone/iPad that way. If I changed the position on my Mac, the position never synced to my iPhone/iPad. I then changed the position on my iPad, and that synced to my iPhone.
All is good now, right? Nope... When I re-opened Safari on the Mac, the bookmark would be at the top of the list again. Then checking my iPhone/iPad, it was back to the top of the list there as well. After doing some troubleshooting, I found that my bookmarks would get reverted just after quitting and re-opening Safari (positions would be forgotten, added bookmarks would be lost, deleted bookmarks would be back). It seemed as if it was only retaining the changes in memory and not getting saved to the disk or iCloud. (And/or pushing the old/corrupt version back to iCloud?)
My bookmarks are syncing fine between my iPhone and iPad though (both on iOS/iPadOS 15.4), just not to/from my Mac reliably.
I thought I had it fixed this morning by disabling Safari syncing, deleting my Bookmarks.plist file, and re-enabling Safari syncing (based on
this thread). All was good for awhile, but it seems to be acting up now that I try it again. (Added a bookmark on my Mac. It added to the bottom of the list this time, but isn't syncing to my iPhone/iPad. Restarted Safari and the bookmark isn't there anymore. Added a bookmark on my iPhone, and that synced to my iPad but not to my Mac.)
Just out of curiosity, do you have a Mac too? Could Safari on the Mac actually be the culprit? Not sure if we're having the exact same issue, but Safari on the Mac seems to be the problem child for me.