In Hauptwerk v7+ you can assign a function to a piston either globally, or for the current organ. Based on your description I think you must have both assigned, in which case the per-organ one will override the global one. Here's the excerpt from the v7 release notice that described that:
As in previous versions, Hauptwerk has on-screen virtual piston toolbars which can be docked around the virtual console window, to allow convenient access to its menu/master functions for touch-screen users, and you can/could (re)assign functions to those virtual piston toolbars’ pistons by right-clicking on them. In previous versions, such function assignments were always on a per-organ basis, i.e. functions that you assigned to them within one organ would not affect assignments within any other, so you would need to assign functions to them separately for every organ (even if you always wanted the same functions to be assigned to them).
However, in v7+ when right-clicking on a piston toolbar piston, a menu/master function may now be assigned to it either globally ('for all organs, unless overridden') and/or only for the currently-loaded organ, with any such per-organ assignment overriding the global assignment for that particular piston toolbar piston, for that particular organ. That avoids the need to duplicate the same function assignment for every organ, in cases where you usually (or always) want the same function to be available on a given piston toolbar piston, whilst still allowing you to customize (override) the assignment in case you want to do that for certain organs.
There is also a right-click menu option to clear an overridden function assignment (if any). By default, when loading a new organ for the first time (ever), global assignments are not overridden for it, i.e. the global assignments apply by default. However, if loading an organ that had been loaded in a previous Hauptwerk version, the organ’s existing per-organ assignments will be migrated and retained.
There are new options on both the General Configuration Wizard and the Organ Configuration Wizard for resetting piston toolbar menu function assignments (globally, and where overridden for the currently-loaded organ, respectively). If you’re upgrading to v7 from an earlier version (for which piston toolbar function assignments were always per-organ), and you now instead wish to assign functions globally, then for each organ in turn you should use “Organ settings | Organ Configuration Wizard” with the “Clear piston toolbar menu function assignments that have been overridden for this organ, and customized names" option ticked (unticking all other options, unless you specifically want to clear anything else too).
I've highlighted in bold the portion above that covers how to clear all such per-organ assignments for the currently-loaded organ, which should allow the global assignments to take effect for that organ.
Alternatively you could right click on the relevant individual toolbar pistons and select the "Clear overridden menu function assignment (for this organ only)" option.