I'm encountering an issue where new files pulled from a subtree are being placed in the root of the repository, rather than the local relative path as specified in the Add / Link SubTree dialog.

If I move these files to their proper location, and pull changes, the files are updated in the correct location.

This may be related to this discussion on stackoverflow; http://stackoverflow.com/questions/1306595/git-confused-when-merging-an-update-into-my-subtree.

From the accepted answer

citation
Unfortunately this is a bug (or missing feature) in the "git merge -s subtree" code. It actually guesses the subtrees that you want to merge. Usually, this magically turns out to be correct, but if your subtree contains a lot of changes (or was originally empty, or whatever), then it can fail spectacularly.
citation

The folder was originally empty, but subsequent pulls that contain new files still drop those new files in the root.

The paths I have been using;

Shared code repo is at

\\DISCOMBOBULATOR\Repository\Visual Studio\Common\TAA Interfaces

Main repo is at

\\DISCOMBOBULATOR\Repository\Visual Studio\biotools

Initial setup for Local Relative path when defining the subtree is

\\DISCOMBOBULATOR\Repository\Visual Studio\biotools\Common\TAA Interfaces

When when viewed after saved is recorded as

Common\TAA Interfaces.

More discussion at https://answers.atlassian.com/questions/282022/subtree-pull-hangs-or-pulls-into-the-wrong-folder