Using Push or Pull from the sprocket cog menu results in Permission Denied (public-key). Git Pull and Push from the terminal works ok inside Aptana.
Everything was working correctly before the upgrade to 3.6.
Keys are still listed in Preferences but now Aptana is looking for the id file in
C:\Users\<username>\Documents\Aptana Studio 3 Workspace\.metadata\.plugins\com.aptana.portablegit.win32\.ssh
It ignores the preferences (mine were and are still set to a network drive so I can roam from PC to PC). If you move your ssh key and known hosts file into this new location, everything works as it did with the old versions.