I'm having the same problems. I'm syncing 2 desktop clients and 1 iPhone client. I'm not syncing the iDisk. I am using MobileMe. I am syncing my OmniFocus database to
https://idisk.me.com/USERNAME/Backup/
It has happened twice to me in the past 12 hours.
Even after I would think I had gotten all reset and had a good sync going, one of two problems would crop up.
1. Even though all clients appeared to be syncing, any changes made on one client wouldn't propagate to the other clients.
2. After a couple of syncs I would get a message saying that there were no root transactions. If I looked directly into the package contents of the database on my iDisk, there would be the client files, but no database files.
I solved it the first time by reverting to a backup that was done earlier in the day. I replaced the server copy with that copy and then propagated it to my other clients.
Then it happened again this afternoon (the first occurrence was last night). This time, on the iPhone I told it to use the local copy, thereby overwriting the server copy with the one on the iPhone. I then propagated that copy to the other clients and it seems to be working, FOR NOW.