osx 10.4 - ~/.ssh/id_rsa doesn't work, whereas ~/id_rsa does

Question

I'm having a strange problem with sshing into a remote box with a private key:

$ ssh me@remote
Permission denied (publickey,gssapi-keyex,gssapi-with-mic).
$ ssh -i ~/.ssh/id_rsa me@remote
Permission denied (publickey,gssapi-keyex,gssapi-with-mic).

Then when I copy .ssh/id_rsa into the home directory (up a level), it works:

$ ssh -i ~/id_rsa me@remote
Enter passphrase for key 'id_rsa':

I don't think the permissions for the .ssh folder have changed at drwxr-xr-x

This is affecting other programs such as Aquamacs which I think looks in .ssh/id_rsa for the key when connecting using tramp.