Applications Folder Problems/Duplicate Icons

I recently managed to do a secure delete with the Applications Folder and all of its contents in the trash. I had recently backed up my system so I restored the lost programs and thought everything was fine, and for the most part, it is. However, when I open some programs that are in my dock from the applications folder instead of just clicking the icon in the dock, then a second icon appears in the dock. The new icon will show that the program is running while the original icon does not. I've included a screen shot showing an example with the Word icons.

I clicked "Show in Finder" for both the programs. I'm not sure if the file paths are actually different or if they just look different to me. Here's a screen shot showing them both:

Now, one other detail— iCal does not open a new icon when I open it from the applications folder, but when a reminder from iCal pops up then a new icon does open.

THINGS I'VE TRIED
I ran disk repair hoping that would fix the glitch, but no luck.
I ran the command killall dock in Terminal, no luck.
I tried logging in as a guest users and seeing if I could duplicate the problem, but a lot of the [/INDENT]programs causing the problem were not available.

Any ideas on how to stop this? I know it's not a big deal, but it is annoying! I'm also worried I caused more damage than I realized, and I want to correct things before larger problems surface.

Try removing applications icons from the Dock, then restarting. Put the ones you want back and see how it goes.

The Dock contains mere aliases. Maybe opening from the Dock they look for the original Application, then open the replacement? Do as toMACsh suggests, remove Dock icons, and replace by dragging from the Applictions Folder.