Your comments
Because the log already shows the stash commits, this request seems covered by http://smartgit.userecho.com/topics/27 and http://smartgit.userecho.com/topics/28.
Do you mean independent repositories or submodule repositories inside one outer repository?
Implemented because now it can operate on the selected files.
Removing these options currently is only possible by editing the global .gitconfig file in the %USERPROFILE% directory using a text editor.
Do you know that you can open the log for repositories without opening them?
Customer support service by UserEcho
Please distinguish between 2 windows and 2 instances. If 2 instances of SmartGit are running (with the same settings directory), this is a bug. But 2 or more windows is by-design.