Mariette,

>> create a folder in the file manager that is stored in the Database and use Documents to upload a file it flips the folder back to insecure
The file manager is part of the core.  The UrlControl that manages uploads is part of the core.

>> act strange when you try to download it, it says that it is going to download linkclick.aspx
The linkclick handler is part of the core.

None of the problems you have mentioned are part of the documents module.  But the core team members read this forum, so I'm sure they are being addressed.

During the period where DNN is a release candidate, your best bet is to report problems in the forums, and wait patiently.  It is not reasonable for you to "give up" until you are working with a final release.