Before using the SourceTree Options dialog, my .gitconfig proxy settings look like this:

[http]
proxy = http://not.my.real.proxy.net:8888
[https]
proxy = http://not.my.real.proxy.net:8888

 
After opening the options dialog and closing, it either using the OK button or the close button in the title bar, my .gitconfig proxy settings look like this:

[http]
[https]
proxy = http://not.my.real.proxy.net:8888

This breaks Git operations that use the network for me.