I updated to Snow Leopard and also updated Skim to 1.2.7. I am a MobileMe user. The Skim notes that I created on the files on my iDisk while using my Macbook were available on my iMac via iDisk sync. New notes that I created after the updates are not syncing through MobilMe anymore. The old notes that were created using old version of Skim in OS X 10.5 are still available.
Sounds more like a MobileMe bug than a Skim bug. We didn't change anything. And I can't imagine Apple would willfully regress on this, because this is something new rather than old. Perhaps you should send a bug report to Apple about this, the key thing is that Skim saves nots in Extended Attributes, so those should be synced and apparently aren't (at least in one way). I cannot test this myself unfortunately.