So the 32- and 64-bit versions of PluginManager.exe have the same filename, just installed into different folders? I'm asking because I don't have 64-bit SONAR installed here.
Next question would be where the menu information is stored in the registry. I'm guessing if there is a separate 64-bit plugin manager the tools menu isn't in the same place as for the 32-bit version, where the path is HKLM\Software\Cakewalk Music Software\Tools Menu. Is there an entry there for the plugin manager?