I have Scrivener for Win 1.7.3.0 (NaNoWriMo trial ver…) running on Win 7 64bit. 8)
When choosing New project from Template, if I choose a directory other than the default Windows Documents, in my case the Google Drive directory, the project opens empty (no root note with template help, empty template sheets, etc.). 
I read in an earlier (June?) post that this bug will be squashed in a later version. Is it still planned for the future? In that case sorry for nagging. 
This may also be a result of a well-known problem with Google Drive itself. I suppose the bright side is that you found out about it while creating a new project.
As for the bug you mention, I’m less familiar with the particulars, if you’re seeing this happen in folders that are not manipulated by third-party software, then we may still have a problem there.
Thanks AmberV,
The problem appears only on “manipulated” directories like Drive and Box, where it manifests not in empty templates but rather that Box refuses to sync the project directory and files altogether.
Choosing the alternative method of backup to cloud syncing seems like the best solution for me.
So it’s not a bug after all, but could Scrivener add a feature warning users before attempting to open a project in a manipulated directory (even Dropbox) and referring them to the excellent Knowledge Base article? I can’t imagine myself looking through the Knowledge Base for help on cloud syncing before opening a project there, it seems the most natural thing to just go ahead and do it.
However better late than never and thanks again for the reference 