Committing sub-repos version change will delete them

The repository I'm using is : http://github.com/artofsequence/aos-all/

I can't pull changes from sub-module from SourceTree but I did it repo by repo using tortoisegit.
Then I switch to sourcetree and I can see the changes in this repository which basically are just change of sub-repo versions.
However, if I commit, it commits deleting the sub-module directories.

I didn't find a way to fix this. (had to reset my version)

Notice that if I commit the same change in tortoisegit, I correctly got just changes on submodule verions when I look at it in SourceTree.