My mac running Snow leopard 10.6.8 is having trouble handling it's ssh keys.

I could previously access all my git repo's via Tower without an issue. The other day I ran Meerkat to see what it was about and it looks like it has broken the way ssh works.

Terminal doesn't seem to have a problem and can still connect to Git, but it can't access the keychain. Tower doesn't seem to be able to access anything.

The Tower support crew have been super helpful, but I wanted to float this here and see if anyone has any ideas on how to fix my problem.

The only hints I have are:

$ which ssh

returns:

/usr/bin/ssh

and

echo $SSH_AUTH_SOCK

returns:

/tmp/ssh-nBhRYVEg8t/agent.199

(This one seems to be wrong as I think it's supposed to point to a Listener, but no idea how to fix it)

additional: Keychain first-aid finds no problems. The problem seems to be that ssh-agent is not being run properly... but that's just a guess.