I've just installed nexus on win 7 64 bit.

Unfortunately, both the Atom text editor and Opera browser do not display as running on the dock, and clicking them opens a new instance of the app (or new tab in Opera) instead of restoring them.

Is this unusual, and is there a fix for it?

My guess is that this is a 32 bit/64 bit vs. file redirection issue, i.e.;:

Either the path to the applications in the dock is C:\Program Files\ and the application running is actually the 32 bit version located at C:\Program Files (x86)\, _OR_ the path in the dock is C:\Program Files (x86)\ but the application running is the 64 bit version located at C:\Program Files\

Hope this makes sense to you, since 32 bit executables of applications are NOT the same as their equivalent 64 bit executables.

You can use the Processes tab of the Windows Task Manager to find out if the running application is 32 or 64 bit (it will say *32 next to the process name if 32 bit) and then adjust the path of the item in the dock accordingly (C:\Program Files\ for 64 bit applications, C:\Program Files (x86)\ for 32 bit applications).