How can I get Quartz Composer to save files after the first time?
After some trial and error, I discovered that Quartz Composer has a problem with directories that have a Spotlight-related entry in their Access Control List (ACL).

Using Terminal, you can see if a directory has a Spotlight ACL entry with ls -dle and looking for output that contains a _spotlight entry, e.g.:

$ ls -dle ~/Documents
drwx------+ 303 userx  staff  10302 20 Aug 12:21 /Users/userx/Documents/
 0: group:everyone deny delete
 1: user:_spotlight inherited allow list,search,readattr,readextattr,readsecurity,file_inherit,directory_inherit


To get Quartz Composer to save to the directory more than just the first time, remove the Spotlight entry from the directory's ACL with chmod, e.g.:

$ chmod -a# 1 ~/Documents


(here we remove the entry whose index is 1, which corresponds to the _spotlight entry gleaned from the ls -dle command).

Another way to do this is to use the Finder's "Get Info" menu command.  You will see a '_spotlight' entry in the "Sharing &amp; Permissions" section.  Select it and click the "minus" sign button to get rid of it.