I have the Devonthink icon in the dock on my Macbook Air. Usually if I scan or save something to Devonthink without having opened Devonthink first, that icon bounces about a little while Devonthink opens in the usual way. Today, however, a SECOND icon for Devonthink appeared in the dock when I saved a Mail message to Devonthink. The first icon was still there, but unmoved. I only have one copy of Devonthink Pro Office in my Applications folder. I turned everything off and tried again, and this still happened. What is going on? Why do I get a duplicate Devonthink icon?
Do a Spotlight search and make sure you don’t have another copy somewhere on your machine.
Command-clicking an application’s Dock icon will open a Finder window for the app’s folder with the app selected. Doing that for each Dt icon appearing in Dock might help you locate any unnecessary duplicate(s).
Should this be Ctrl-clicking?
Control-click opens the app’s Dock contextual menu. Command-click does what sjk wrote that it does.
And Show in Finder can be found under its Options submenu, which does the same thing as a Command-click on the icon.
See, you do learn something new every day. I have never seen this tip. Thanks, sjk!
And just because it led me to another I hadn’t known…
Command-Option click the dock icon of an application to switch to the app and hide others in the current Space. If the app is not running it will launch and hide the others.
(Note: I am on my Lion machine right now so I can’t vouch for Mountain Lion right now).
Man, I love Macs. 
Over here on 10.8.3 command-option-click-dock icon hides everything on all the other desktops except the one that has the current focus. I am scratching my head wondering why that’s a good thing. 
Maybe it’s supposed to function as a “boss key” (or a “parent/spouse” key - though I am not advocating any naughtiness. 
). Interesting…
It also usually hides everything on the active desktop (space) when there are no open windows for the app on it and System Preferences > Mission Control / When switching to an application, switch to a space with open window for the application is disabled, like running App > Hide Others without making the app active first, but I’ve found some space-switching exceptions. Still with that MC option disabled, which app is activate after running Hide Others from the Dock icon menu and space-switching behavior with Command-Tab app selection can vary. Space-switching methods (with/without implicit app-switching) are generally more predictable and effective for me than app-switching (with/without implicit space-switching).
My only Hide Others usage is accidental, which I’m still prone to doing about monthly mostly with its shortcut mostly in Safari. It was initially startling before realizing what was happening. No boss or parent/spouse key for me. 
Dear all,
Thanks for your suggestions. I didn’t have two DevonthinkPro apps on my computer. BUT for some strange reason (maybe to do with the latest upgrade of Devonthink Pro Office). my ScanSnap Scanner had TWO paths leading to Devonthink Pro Office. I deleted both and set up the ScanSnap to scan to Devonthink again. Now it works perfectly again! – And thanks all for the advice about how to do things with the dock!