I'm having the same issue and it happens in both Sonar x64 and Reaper x64. I haven't renamed any xml files or anything like that and I'm running the latest version of Nebula (UpgradeNebula3 Pro x64 1.3.413.rar), Reaper and Sonar.
Does the license file have to be installed for x64 as well as x86?
I agree with other users, it would be much nicer (at least in the case of Reaper, not sure how Sonar handles this) if the plugin had the same name, so that if you opened up the project in x64 it would use the x64 version and in x86 it would use the x86 version. I don't know if that is possible from a technical perspective???
One thing I have made note of is that past versions some times defaulted to slightly different paths during installation. Try a re-install and pay close attention to the install path. See if you notice anything.
install 1.3.400 setup and run it. Than install 1.3.413 It happens because both 1.3.412 and 1.3.413 have a known bug and it crashes the first time it scans folder. 1.3.413 doesn't scan folders, but you need to run setup 1.3.400 before. I'll upload a fixed version soon.