Hello David,
Did you migrate your existing audio settings/routing to v5 (as opposed to resetting to defaults, when prompted when v5 first ran)?
Also, please try launching Hauptwerk via a a 'spare' 'Hauptwerk (alt config N)' configuration (desktop short-cut), then using 'General settings | General configuration wizard' to reset everything to defaults, then select you standard audio device (not the VST/AU Link), then load one of the organs exhibiting the problem, then use the 'Organ settings | Organ configuration wizard' to reset all settings to defaults. Does it still exhibit the issue? How about St. Anne's?