With OS X 10.9.2 I can’t open any of my Scapple documents from iCloud but if I copy them first on to my Mac they will open just fine. If I try to open document directly from iCloud I get following error “The document “XXXXXX.scap” could not be opened”. With previous OS X versions working with iCloud documents was smooth sailing.
Are you having any issues with other iCloud enabled software, like TextEdit? Also, are you using the direct-sale or Mac App Store version of Scapple?
Restarting seems to solve the problem with 10.9.2 but the problem kept coming back now and then. OS X 10.9.3 (13D17) seems to reliable and I’m not getting any problems with opening Scapple documents from iCloud. The application was bought from App Store.