Steps to reproduce:
1. Clone this repository in SourceTree: https://bitbucket.org/jennings/sourcetree-subtree-does-not-link-on-first-try
2. Click Repository --> Add/Link Subtree
3. Provide a remote URL and branch, and use "sub" as the local relative path. Click OK, then click Create Link.
The subtree should now be visible in the left column under the heading "Subtrees"
The subtree does not appear (the heading is not collapsed). If I quit SourceTree, then immediately repeat steps 2 and 3, the subtree does appear in the left column.
I did a diff of the .git/sourcetreeconfig file between each step, and it does not have the subtree's information written into it until after quitting SourceTree and immediately trying to link the subtree again.