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 -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 & Permissions" section. Select it and click the "minus" sign button to get rid of it.