Since Nisus Writer Pro opens ".doc" files, the Finder has to choose between the two applications to open this file. How does the system determine which application to open these files? Something called Launch Services looks at, among other things, the file extension to determine which application to use to open these files. The official Apple explanation of this phenomenon can be read here.
Note that the system changes the icon only, not the file itself. In other words, nothing has been changed except the icon.
To change the association from Nisus back to Word, simply choose a file that you want to change, then go to the Finder and from the File menu, choose "Get Info". In the "Get Info" window, find "Open with:" and from the pull down menu, choose "Microsoft Word" and that document will be associated with MS Word. If you want all documents of that type to open with Word, click the "Change All..." button.
Nisus Writer Pro can still open those documents, but you will have to drag it to the Nisus icon in the dock or use the Open dialog in Pro.
*This phenomenon occurs in systems earlier than Mac OS X 10.5
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