The rightclick menu for the nicklist is in popups.ini, and that may have been corrupted, or you upgraded from an old version where you had a syntax error which is no longer forgiven.
Is there an error message showing in the server status-window when you do one of those rightclicks? Is it only the nicklist that doesn't work right, or does it no longer give you the right-click menu in the middle of the #channel or in the middle of the "status window"?
Use Alt+P to open the popups tab of remotes script editor, then use that interior 'view' menu to choose the nicklist view. Is it blank? In the lower-left corner of that window, does it show the filename is popups.ini?