Sublime text 3 has some big problems with mounted file systems. This is partially due to the new atomic_save setting. This sublime forum post seems to imply that your problem is caused by atomic save.
Try putting this in your user or project settings:
"atomic_save": false
It seems that when a file is saved with atomic save, a new file is created with the hidden attribute, then the original file is deleted and the temporary hidden file is renamed to replace the original. When you are using a shared filesystem, the hidden attribute must never get reset.