First off - check your Options - Setup (Ctrl+S) - MISC - do you have something defined for SSH? (I use Putty - so, for me, its just c:\putty.exe, which works quite well.)
A) For each device that you have moved to ssh - are you able to connect to them normally - via putty/securecrt/etc?
B) Are you using radius or TACACS+ to manage logins, or are the usernames local to the device? (you only need to use the AAA option if you have a 3rd party authentication like Radius/TACACS.)
C) Have you modified the device record in CatTools (Device Info, Method, Port)which are you selecting? (just verify this. In most cases SSHv2 will work. In some cases you may have to use "Cisco.SSH" or something. -
D) From the CatTools console, pick the device, click on EDIT, and do a test login there.