I would suggest not building Sage in /Applications. I think that the Dock keeps track of all of the files there, and building Sage alters many files, resulting in lots of bookkeeping by the Dock. So keep Sage somewhere else, and have a link to it in /Applications. In fact, if you're not going to use the app version, you don't even need the link there. I build Sage somewhere in my home directory and put a link to the sage executable in /usr/local/bin.