app preview: documents in the dock always in front window

I think I understand now. You have Preview.app open with several windows open and minimized in the Dock. You quit Preview.app and when you reopen it opens all previous windows but they are not minimized.

In System Preferences > General, check Close windows when quitting an app. You can reopen, by selecting File > Open Recent in Preview.

Automatically re-open windows, apps, and documents on your Mac - Apple Support

Do a backup, using either Time Machine or a cloning program, to ensure files/data can be recovered. Two backups are better than one.

Try setting up another admin user account to see if the same problem continues. If Back-to-My Mac is selected in System Preferences, the Guest account will not work. The intent is to see if it is specific to one account or a system wide problem. This account can be deleted later.

Isolating an issue by using another user account

If the problem is still there, try booting into the Safe Mode using your normal account. Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer or by using the developer’s uninstall instructions. For each disable/delete, you will need to restart if you don't do them all at once.

Safe Mode - About El Capitan
also Sierra

Safe Mode Startup – El Capitan. also Sierra

If it works in the Safe Mode, try running this program when booted normally and then copy and paste the output in a reply. The program was created by Etresoft, a frequent contributor. Please use copy and paste as screen shots can be hard to read. On the screen with Options, please open Options and check the bottom 2 boxes before running. Click “Share Report” button in the toolbar, select “Copy to Clipboard” and then paste into a reply. This will show what is running on your computer. No personal information is shown.

Etrecheck – System Information

I'm not exactly sure what you are doing. When you say "preview" do you mean the app Preview or are you referring to Quick Look?

A screenshot might be helpful.

Command-Shift-3 takes the entire screen

Command-Shift-4 takes a portion of the screen.

Click on the camera icon in the toolbar of the reply window to post. Select image to upload.

Be careful not to include any private information.