In SourceTree, Clone seems to bring submodule files from GitHub repos then seems to delete them

Question

I have a Visual Studio solution and its projects are grouped in several GitHub repos, many of them as submodules, something like:

Submodule 1
  files...
Submodule 2
  files...
MainProj
  Submodule A
    files...
  Submodule B
    files...
  Folder 1
    files...
  Folder 2
    files...

If use Clone (recurse submodules checked) from SourceTree graphical interface to bring the solution on disk from GitHub, the content of submodules folders are created empty on disk. If I look in SourceTree, I see that all the files residing in submodules appear in the Staged files with a red, minus icon like they were brought/cloned, then deleted and staged, just not committed as erased. I can Discard them all and then is fine but it takes an incredible amount of time (tens of minutes) because just selecting them triggers a lengthy process. There are many, many big files.

I can use from SourceTree Terminal

$ git clone --recursive <url>

and it works fine so it seems is a problem with SourceTree.