I, too, am having sync problems with Ulysses.
First nine months, all was fine, but then…
I ran into an issue very similar to what @KevinR reported at the top, which is how I came to this page (fixed it with the same “move 'em to a different group” solution he mentioned).
Then, another day, sync was ultra-slow and the iCloud icon on Finder was going nuts as if the system were “thrashing around” trying to find stuff. It finally settled down, but was unnerving to watch.
Most recently, I got the dreaded red-sheet error where it popped up a conflict warning right in the middle of a writing session. Neither of the two choices it gave me was current, but I took the newest one and figured, ah, well, I’ll just rewrite what I lost — only to open the same sheet up on a different device and find all of the lost stuff still there after all. That one is the weirdest of all, at least so far.
So, at the end of this rant, I do have a question: am I snakebit, or does this behavior and what you other posters mentioned simply mean that there is an inherent, long-standing bug in Ulysses’s file storage model that makes it an unreliable vessel for one’s work? I, like @KevinR, have been giving iA Writer that “long, hard, awkward stare,” and for pretty much the same reasons. I already use iA Writer for blogging, and now am wondering whether to move my fiction work to it from Ulysses, as well. My early tests of doing so have been promising, and the non-proprietary, unobscured file storage is like a breath of fresh air.
Will be very grateful for your collective wisdom on this, my friends and colleagues.