I experienced a similar issue in Eclipse (Ganymede), when using the Maven and Subeclipse plugins. I have not determined which plugin caused this problem, but I suspect that it is related to my pom.xml containing nested modules (ie. a main-moduleintegration-test). These appear in Eclipse as nested folders with their own pom.xml files (I did not use the Multiple Projects plugin although I have installed it).
I assume that one of the plug-ins has incorrectly set the derived flag on these folders when I checked out the project by SVN and then updated the MVN dependencies and project settings.
When I right click->properties on the top-level nested module directories I can see the Derived flag is checked. By unchecking the derive flag on the module directories (and checking the derive flag on the target directories within each sub-module instead), it fixed the Open Resource functionality.
As the derived flag is inherited from directories, you may need to check all of your directories in the hierarchy to find the 'culprit'.
If it helps the plug-in authors, my top level module directories contain a hyphen '-' in their names. Maybe that is throwing out one of the plugins.
Cheers,
Alex