For convenience's sake, I keep the non-password protected key constantly loaded in pageant. When I SSH into the box, I explicitly tell PuTTY to use the other key.
With winscp, I'm having some problems where winscp appears to check pageant for a public key first, and use it, even if I have explicitly specified the private key I'd like to use.
Steps to reproduce:
1. Create an SSH account with multiple authorized keys. With one authorized key, define a forced command that boots up some sort of server, such as svnserve, example:
command="svnserve -t -r /svn/repos" ssh-rsa [key data]
ssh-rsa [key data]
(First key is the SVN key, second is the regular key
2. Load the SVN key into pageant
3. Open up WinSCP, fill in the login parameters, select the regular key as the private key
4. Attempt to log in
Expected result: Regular key is used, SFTP works
Actual result: Login works, but SFTP initialization fails due to overly large SFTP packet (i.e. SVN key was used)
Removing the SVN key from pageant fixes the problem.
I recognize that this quite a bit of an edge case, but I think that nonetheless the behavior is a bug: explicit private key should win any day over pageant.