That is gonna be hard to explain but I'll do my best. So I have got say Debian with openssh5.5 using protocol 1(does not really matter, for example RHEL/Fedora's with 5.9 using p1 got the same problem). Got different FreeBSD servers, one of them is using openssh5.4 protocol 1, other one is on openssh5.8 protocol 2. Configuring the rsa key logins succeeds on to the first server, but does not by any means on the second one. I have played all the way around with protocol version settings(at the moment on all the systems I mentioned protocol 2 is used only, and they keep acting differently), auth file names(checked multiple times for them to be correct in configs), rights and anything possible to make it work but close to giving up now. ssh-agent is working everywhere, sockets and pids are fine. I have commented out everything in my sshrc's because they like to cause various problems. Created all possible types of the key: rsa(which, if I am correct, should be the one I need for 2 protocol?), rsa1, dsa and ssh-add'ed them(-l checked for 200% confidence). What else to look at? The one thing I do not really get, is why
# ssh -v
gives me strict version, say 1.5-2 or alike, while the configure files allow the selection and probably(or not?) support the 2nd protocol regardless of version output. Maybe my head is generally messed up abit, if I have forgotten to mention something and this could help, please ask any questions.