I'm using SourceTree 18.104.22.168 on Windows 7 Enterprise SP1.
I have a private key file that I generated with PuttyGen and saved to a file with no file extension. I can load the file fine from Pageant and SSH functions in SourceTree work fine after doing so.
I have configured the SSH Key option in SourceTree with the path to my PK file.
However, the key is not loaded into Pageant when SourceTree launches Pageant during startup. I am also prompted to load the key file if Pageant is not running and I use the Launch SSH Agent... function from the Tools menu. If I say Yes and browse to the file, the SSH Key option is automatically configured with the correct path to the extensionless file, as I would expect.
If I add the .ppk extension to the file everything works as expected. Pageant is launched during SourceTree startup and my key file is loaded by Pageant. Also, launching Pageant from the command line with the path to the extensionless file works fine.
This is clearly not high priority issue, rather a minor annoyance, but I thought I would submit something on it anyway.
Bug reported: https://jira.atlassian.com/browse/SRCTREEWIN-6187
Have you tried launching pageant from the command line using a parameter to have it immediately load the key? This is probably what SourceTree does behind the scenes, and if pageant doesn't load the key when specified on the command line, it's a pageant issue, not a SourceTree one.
However, if that works fine, you should submit a bug report to jira.atlassian.com.
If you want to quit relying on SourceTree to launch Pageant, you can follow these steps to get Pageant to launch with your key: http://blog.shvetsov.com/2010/03/making-pageant-automatically-load-keys.html
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