@Jonathan See if discourse#4523 helps (make sure your theme is on remote server, update your rsync version, and deal with subtree variable if necessary). I’m not sure which version of Trellis you are using, so note that since that thread, the subtree variable was renamed subtree_path on Sep 6, 2015, then repo_subtree_path on Dec 29, 2015.
See also discourse#4029
If your Trellis version is as new as Dec 28, 2015 and roots/trellis#454 hasn’t yet been merged, you could see if it helps to edit your hosts/development file:
- 127.0.0.1
+ 127.0.0.1 ansible_connection=local